In this study we investigated virus-virus and vector-virus interactions by combining two approaches:

  1. meta-transciptomic analysis, and
  2. gene-silencing experiments.

In the following code pipeline we present the (1) meta-transcriptomic analysis.

Here we looked at the overall viral landscape in the different libraries, detected vector modules (co-expressing genes using gene-network analysis), and correlated the viruses’ abundance to the vector modules. Last, we tested if the virus abundance matrix can predict the virus-vector interaction.

In this R markdown document we present the meta-transcriptomic analysis step by step in a way that can be reproduced using the input files available on the GitHub web-page. The following chunks are ordered as the sections in the Materials and Methods of the manuscript “Diverse and rapidly evolving viral strategies modulate arthropod vector gene expression”, Eliash et al. (2022). All of the referred tables and figures can be found in the manuscript as well.


RNAseq data collection, mapping and filtration

Sequence Read Archive (SRA) data collection

We searched for the term “varroa” in the SRA databases (NCBI, January 2020) with the following filters:

  • Source: “RNA”
  • Library Strategy: “RNA-seq” (Random sequencing of whole transcriptome)
  • Library Source: “TRANSCRIPTOMIC”, “VIRAL RNA”
  • We included only whole mites (partial organs not included)

Reads mapping and transcripts quantification

The reads were mapped to both available varroa genome (Vdes_3.0, accession number: GCF_002443255, (Tehcer et al. 2019)), and to the genomes of 23 selected viruses (table 1). The alignment and estimation of transcript and virus abundances were done using Kallisto (Bray et al. 2016) (version 0.46.1 with default options). The abundances were outputted in transcripts per million (TPM) units.

Load data and RNAseq library filtration

Load libraries

library("dplyr")
library("tidyverse")
library("vegan")
library("DESeq2") 
library("ggfortify")
library("WGCNA")
options(stringsAsFactors = FALSE) # Allow multi-threading within WGCNA. This helps speed up certain calculations.
library("rmarkdown")
library("knitr") # for the markdown
library("kableExtra") # for creating a scrolling table
library("ggplot2") # for plotting 
library("ape") # for mantel.test
library("Biostrings")
library("ggrepel") # for spreading text labels on the plot
library("scales") # for axis labels notation
library("GO.db") # for GO term annotation 
library("reshape2")
library("RSQLite")
library("AnnotationDbi") # for GO term annotation 
library("GSEABase")
library("GOstats")
library("maps") # for the map background
library("htmltools")
library("rgdal")
library("grid")
library("gridExtra")
library("GeneOverlap") # for making the overlapping genes
library("cluster")
library("rmdformats")
library("corrplot") # for virus-virus correlation
library("viridis")
library("hrbrthemes")
library("ggthemes")
library("RColorBrewer")
library("naniar")
library("kableExtra")
knitr::opts_chunk$set(echo = TRUE)
setwd("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks") #set the directory as the local GitHub local repository

Create the initial input data frame

The mapped libraries were used to create the initial data frame, in which each column is a SRR library, and each row is an isoform. The cells contain the isoform TPM.
The output data frame contains 35,669 isoforms of the selected 71 varroa libraries. The first 35,641 rows are varroa genes, and the last 28 rows are reads that matched to the selected viruses (for viruses’ details, see Table 1).

# First make a function for making the mapped reads (output of kallisto) into a data frame
read_kallisto <- function(filename) {
  sampleName <- sub("data/kallisto/(.*).tsv.gz","\\1", filename)
  return(read_tsv(filename) %>%
           dplyr::select(!!sampleName := tpm))
}

# now make the data frame, which contain all 71 libraries: 
df_71 <- list.files(path = "data/kallisto", full.names = TRUE) %>% 
  lapply(read_kallisto) %>% 
  bind_cols() 

# add a column "target_id" with the isoform/virus ID
df_71$target_id <- list.files(path = "data/kallisto", full.names = TRUE)[1] %>% 
  read_tsv() %>% 
  dplyr::select(target_id) %>% 
  pull()

#save(df_71, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/kallisto_71.rds")

Join varroa isoforms into genes

# Next, we join isoforms that belong to the same gene.

# Load the data frame created in the former chunk 
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/kallisto_71.rds")

# Import the varroa transcripts ("target_id") and their corresponding gene ("gene_id").
varroa_isoforms <- read_tsv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/gene2isoform.txt.gz", col_names = c("gene_id", "target_id"))

# Join the varroa transcripts (varroa_isoforms), and the library tpm (df), by the isoform ID ("target_id"). As we do "left_join", the final data frame of "gene_tpm" contain ONLY varroa genes, excluding viruses' tpm. 
gene_tpm_71 <-  left_join(varroa_isoforms, df_71, by = "target_id")

# Collapse isoforms ("target_id") to a single row of a gene ("gene_id"), and sum the tpm(s) per gene per library
gene_tpm_collps_71 <- gene_tpm_71 %>% 
  gather("library","tpm", -target_id, -gene_id) %>%
  group_by(gene_id, library) %>% 
  summarise(gene_tpm_71 = sum(tpm)) 

# spread the table again, by library
final_gene_tpm_71 <- spread(gene_tpm_collps_71, key = "library", value = "gene_tpm_71") %>% column_to_rownames('gene_id')

# this table will be used for all further analyses
# save(final_gene_tpm_71, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/final_gene_tpm_71.rds")

Next, we perform Principle Component Analysis (PCA) on varroa genes, to detect outlierd libraries

Detect outlier libraries based on PCA (Figure S2)

# load the table
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/final_gene_tpm_71.rds")
     
# Before PCA, we transpose the table "final_gene_tpm_71", and transform (log10+0.000001) 
final_gene_tpm_71_T<- transposeBigData(log10(final_gene_tpm_71 + 0.000001))

PCA_71 <- prcomp(final_gene_tpm_71_T)
p71 <- autoplot(PCA_71, label = TRUE, x = 1, y = 2)+
  ggtitle("a. PCA of 71 libraries based on gene expression")

# Five libraries are obvious outliers: "SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385".
final_gene_tpm_66_T <- final_gene_tpm_71_T %>%
  rownames_to_column("library") %>%
  dplyr::filter(!(library %in% c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385"))) %>% column_to_rownames("library")
PCA_66 <- prcomp(final_gene_tpm_66_T)
p66 <- autoplot(PCA_66, label = TRUE, x = 1, y = 2)+
  ggtitle("b. PCA of 66 libraries based on gene expression")
# plot the two PCA plots side by side:
par(mar = c(4, 4, .1, .1))
p71  
p66 

# when we remove them and repeat the PCA (Fig S2b), the library scatter more homogeneously.
Figure S1. PCA of varroa SRA libraires based on their genes TPM. a. All 71 libraries. The outlier libraries can be seen on the left side of the plot. These 5 libraries were excluded from further analysis. b. the final 66 libraries used for the analysis.Figure S1. PCA of varroa SRA libraires based on their genes TPM. a. All 71 libraries. The outlier libraries can be seen on the left side of the plot. These 5 libraries were excluded from further analysis. b. the final 66 libraries used for the analysis.

Figure S1. PCA of varroa SRA libraires based on their genes TPM. a. All 71 libraries. The outlier libraries can be seen on the left side of the plot. These 5 libraries were excluded from further analysis. b. the final 66 libraries used for the analysis.

After filtering outlier libraries (based on PCA analysis), we used the left 66 SRAs belonging to 9 studies of varroa RNAseq for further analyses (details of the final libraries available in Table S5).

Remove outlier libraries and save data frame of varroa genes for later WGCNA

# We remove the five outlier libraries from the data frame, and save for subsequent analyses 
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/kallisto_71.rds")
df <- df_71 %>% dplyr::select(-c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385"))

# In addition, we save the final varroa genes TPM values per library, of the filtered 66 libraries, for the Gene Network analysis.
for_modules <- final_gene_tpm_71 %>% 
  dplyr::select(-c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385")) %>%
  transposeBigData() 
#save(for_modules, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/for_modules.rds")

Viral abundance analysis

AIM: describing viruses’ abundance in the different varroa SRA libraries.

We first prepare the suitable data frame containing viruses’ load in each library, by joining the initial df, with viruses’ IDs:

# read the viruses IDs:
virusId <- read_tsv("data/viruses.txt", col_names = c("target_id", "description"))

# Varroa orthomyxovirus-1 (VOV-1) virus genome has been described in 6 different segments (Levin et al. 2016). Before proceeding for viral abundance analysis we sum all VOV-1 segments into one.
virusId[3:8, 2] <- "VOV_1"
x <- left_join(virusId, df, by = "target_id") %>% dplyr::select(-target_id) 
# Sum all 6 segments TPM in each library in a separate table 'VOV_1':
VOV_1 <- x %>% 
      dplyr::slice(3:8) %>%
      group_by(description) %>%
      summarize_all(sum)
#filter out the segments of VOV_1,  
x <- dplyr::filter(x, description != "VOV_1")
# insert VOV_1 in row 3 
r <- 3
insertRow <- function(x, VOV_1, r) {
  x[seq(r+1,nrow(x)+1),] <- x[seq(r,nrow(x)),]
  x[r,] <- VOV_1
  x
}

viruses_load <- insertRow(x, VOV_1, r)
head(viruses_load)

# save the viral load data frame
#save(viruses_load, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load.rds")

Figure 1. Vizualize viruses distribution and abundance in a heat-map

# (3) heat-map of viruses loads (log10(tpm)) per library
# load the former virus data
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load.rds")
# plot the viruses abundance in each library
# make a vector of the new viruses order
new_order <- c("DWVa", "VDV1/DWVb", "VDV2", "BMV","VOV_1","ARV_2", "DWVc", "AmFV", "VDV3", "ABPV", "VTLV", "SV", "BQCV","VDV4", "IAPV", "KBV", "SBPV", "LSV","CBPV" ,"AFV", "ANV", "VPVL_46","VPVL_36")

# re-order the viruses, based on viral load and viral abundance (from highest, on the left, to lowest on the right), and change the names of the viruses to match their common name in the literature:
viruses_load_arranged <- viruses_load  %>%
  mutate(description =  factor(description, levels = new_order)) %>%
  arrange(description) %>%
  mutate(across("description", str_replace, "VOV_1", "VOV-1")) %>%
  mutate(across("description", str_replace, "ARV_2", "ARV-2")) %>%
  mutate(across("description", str_replace, "SV", "SBV")) %>%
  mutate(across("description", str_replace, "LSBV", "LSV")) %>%
  mutate(across("description", str_replace, "VDV1/DWVb", "DWVb"))

# lock in factor level order
viruses_load_arranged$description <- factor(viruses_load_arranged$description, levels = viruses_load_arranged$description)

# spread the df 
virus_abund <- viruses_load_arranged %>%  
    gather("library", "tpm", -description) 

virus_abund[, 3] <- (virus_abund[,3]+ 0.000001) # I added 0.000001 to each value, so there will be no zeros
virus_abund[, 3] <- log10(virus_abund[,3]) # tpm in log10 scale
virus_abund <- replace_with_na(virus_abund, replace = list(tpm = -6)) # whenever there is a zero value (-6), I replace with NA, so the cell will appear in gray color.

# now make a heat map
ggplot(data = virus_abund, mapping = aes(x = description,
                                                       y = library,
                                                       fill = tpm)) +
  scale_fill_gradient2(low="#FFFFCC", mid = "#FF9933", high="#990000",  na.value = "grey92") +
  geom_tile() +
  theme_linedraw() +
  xlab(label = "Viruses") +
  ylab(label = "Varroa SRA libraries") +
  labs(fill = "Viral load \n log10(TPM)") + 
  theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 15)) + 
  theme(axis.text.y = element_text(size = 12)) + 
  theme(axis.ticks = element_blank()) +
  theme(axis.title = element_text(size = 20))
Figure 1. Viral load is diverse across the different varroa libraries. Values are log10 transformed of the reads’ TPM (transcript per millions). Zero values are marked in grey (i.e., none of the reads in this library mapped to this virus). The viruses’ names are abbreviated as described in Table 1.  More information on the viruses’, accession numbers, genome length, references and etc. are available in supp table S1. Members of the Iflavirus family are the most prevalent, yet while some viruses are homogenous across libraries (VDV2), others are highly diverse (e.g. DWVa and DWVb).

Figure 1. Viral load is diverse across the different varroa libraries. Values are log10 transformed of the reads’ TPM (transcript per millions). Zero values are marked in grey (i.e., none of the reads in this library mapped to this virus). The viruses’ names are abbreviated as described in Table 1. More information on the viruses’, accession numbers, genome length, references and etc. are available in supp table S1. Members of the Iflavirus family are the most prevalent, yet while some viruses are homogenous across libraries (VDV2), others are highly diverse (e.g. DWVa and DWVb).

Figure 2a. Virus correlation matrix

the viral correlation analysis includes 66 libraries, and 15 viruses (viruses that appear in at least one of the libraries)

load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load.rds")

# prepare the 'viruses_load' table, with 15 viruses, 
# excluding viruses with 'zero tpm': "CBPV", "AFV", "ANV" , "VPVL_46", "VPVL_36", "SBPV", also excluding viruses with low abundance :"KBV", "LSV".  left with 15 viruses
viruses_load_15 <- viruses_load %>%
  filter(description %in% c("DWVa", "ARV_2","VOV_1", "BMV","AmFV","ABPV","VTLV","IAPV","SV","VDV1/DWVb","DWVc","BQCV","VDV3","VDV2","VDV4")) %>%
  column_to_rownames("description") %>% 
  transposeBigData() %>%
  rownames_to_column("library") %>%
  #identify and remove the row numbers of the outlierd libraries (found by PCA) 
  #filter(!(library %in% c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385"))) %>% 
  column_to_rownames("library")

# make a function to correlate viruses load
corrplot2 <- function(data,
                      method = "pearson",
                      sig.level = 0.05,
                      order = "original",
                      diag = FALSE,
                      type = "upper",
                      tl.srt = 75,
                      number.font = 1,
                      number.cex = 0.5,
                      mar = c(0, 0, 0, 0)) {
  
  data_incomplete <- data
  data <- data[complete.cases(data), ]
  mat <- cor(data, method = method)
  cor.mtest <- function(mat, method) {
    mat <- as.matrix(mat)
    n <- ncol(mat)
    p.mat <- matrix(NA, n, n)
    diag(p.mat) <- 0
    for (i in 1:(n - 1)) {
      for (j in (i + 1):n) {
        tmp <- cor.test(mat[, i], mat[, j], method = method)
        p.mat[i, j] <- p.mat[j, i] <- tmp$p.value
      }
    }
    colnames(p.mat) <- rownames(p.mat) <- colnames(mat)
    p.mat
  }
  p.mat <- cor.mtest(data, method = method)
  col <- colorRampPalette(c("#053061","#2166ac","#4393c3","#92c5de","#d1e5f0","#f7f7f7","#fddbc7","#f4a582","#d6604d","#b2182b","#67001f"))
  corrplot(mat,
    method = "color", col = col(200), 
    mar = mar, 
    type = type, order = order,
    tl.col = "black", # replace with "white" to hide the viruses names, as in the plot for the MS. 
    # hide correlation coefficients on the diagonal
    diag = diag
  )
}

# plot the correlogram
virusAbundCor_66 <- corrplot2(
  data = viruses_load_15,
  method = "pearson",
  sig.level = 0.05,
  order = "original",
  diag = F, 
  type = "upper",
  tl.srt = 75)
Figure 2a. Correlation between viruses’ loads. P-values of the Pearson coefficient are adjusted according to FDR-correction; correlation significance marked by (*) 0.1 < Padjust < 0.01; (**) Padjust < 0.01. All viruses’ loads are transformed by log10 of the (TPM), Transcripts Per Million.

Figure 2a. Correlation between viruses’ loads. P-values of the Pearson coefficient are adjusted according to FDR-correction; correlation significance marked by (*) 0.1 < Padjust < 0.01; (**) Padjust < 0.01. All viruses’ loads are transformed by log10 of the (TPM), Transcripts Per Million.

# save the matrix for future analysis (Mantel)
#saveRDS(virusAbundCor_66, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/virusAbundCor_66.rds")

# and the table of viral load of the 15 viruses in 66 libraries:
#save(viruses_load_15, file = "results/viruses_load_15.rds")

Gene network analysis

We used a network analysis approach to identify groups of genes that share a similar expression pattern across a large set of available varroa transcriptomic data (RNAseq). To construct the gene-network, a weighted gene co-expression analysis was carried out using the WGCNA package in R, following the authors’ tutorial (Langfelder and Horvath 2016; Langfelder and Horvath 2008).

The gene network analysis included 4 main steps:

  1. Network construction and module detection
  2. Correlating modules to external information, the varroa viral load
  3. Identifying important genes, ‘hub-genes’
  4. GO-term enrichment analysis for varroa modules which interact with the viral load

A gene co-expression network is a a systems-biology approach, based on the assumption that biological functions are carried out in a modular manner (Barabási and Oltvai 2004). We identify co-expressed genes that have similar expression patterns across samples using hierarchical clustering and place them in gene groups, called ‘modules’ (Stuart et al. 2003).

(1) Network construction and module detection

Following the steps in WGCNA tutorial: “Automatic, one-step network construction and module detection” (Langfelder and Horvath 2016)

Choosing the soft-thresholding power: analysis of network topology (Figure S1a)

For the varroa Gene network analysis we gonna use the “for_module” file created in the chunk “PCA” of section “Load data and library filtration”. This data frame is the initial input for all the WGCNA, and contains the varroa genes TPM, where columns are genes’ ID and rows are the RNAseq libraries

load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/for_modules.rds")

# Take a look at the data frame (print 5 genes in 10 libraries): 
head(for_modules[,1:5], 10)
##            111242787  111242788 111242789 111242790 111242792
## SRR3632582  16.69060 13115.3000  1.632676   4.68461  39.04070
## SRR3633003  27.71050    68.2067  1.006694   8.47756  86.32650
## SRR3634700  30.52360    37.5802  1.105930   7.45524  45.91280
## SRR3634772  39.17820   246.4390  3.671050   9.14239  48.84960
## SRR3634929  12.14060 74095.9000  9.223820   3.01799  20.93230
## SRR3634942  22.61910    12.7722  2.068261   7.35609  51.97150
## SRR3635001  34.69800    19.2896  1.312841  10.61080  58.61030
## SRR3635050  11.08990 85335.2000  9.115974   2.16917  17.92070
## SRR3635105  29.92650   253.0850  2.128474   7.89757  50.31910
## SRR3927486   7.45717  3993.3700  1.491740   1.11916   7.85349
# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to=25, by=2))
# Call the network topology analysis function
sft = pickSoftThreshold(for_modules, powerVector = powers, verbose = 5)
## pickSoftThreshold: will use block size 4366.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 4366 of 10247
##    ..working on genes 4367 through 8732 of 10247
##    ..working on genes 8733 through 10247 of 10247
##    Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
## 1      1  0.84900  1.9000          0.807  3610.0    3730.0   5270
## 2      2  0.54000  0.6600          0.894  1910.0    1920.0   3460
## 3      3  0.00867 -0.0596          0.507  1200.0    1150.0   2540
## 4      4  0.22700 -0.3920          0.527   826.0     820.0   1970
## 5      5  0.35500 -0.6060          0.599   603.0     603.0   1580
## 6      6  0.42100 -0.7390          0.652   459.0     446.0   1300
## 7      7  0.45200 -0.8360          0.675   359.0     337.0   1080
## 8      8  0.49200 -0.8910          0.695   288.0     257.0    916
## 9      9  0.49900 -0.9460          0.682   236.0     199.0    787
## 10    10  0.51500 -0.9400          0.646   196.0     157.0    684
## 11    12  0.88600 -0.8650          0.973   141.0      99.9    557
## 12    14  0.87200 -1.0800          0.922   106.0      66.2    521
## 13    16  0.87100 -1.2100          0.871    82.4      44.8    491
## 14    18  0.86000 -1.2900          0.824    65.9      31.3    465
## 15    20  0.85000 -1.3200          0.809    53.9      22.2    442
## 16    22  0.84800 -1.3300          0.822    45.1      16.2    422
## 17    24  0.84000 -1.3200          0.840    38.4      11.9    404
# Plot the results:
sft_df <- data.frame(
  Power = sft$fitIndices[,1],
  sft_signedR2 = -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
  mean.k = sft$fitIndices[,5])

# Scale-free topology fit index as a function of the soft-thresholding power
pSI <- ggplot(data = sft_df, aes(x = Power, y = sft_signedR2, label = Power)) + 
       xlab("Soft Threshold (power)") +
       ylab("Scale Free Topology Model Fit,signed R^2") +
       ggtitle("Scale independence") +
  theme_classic() +
  theme(text = element_text(size=16)) +
  geom_text(data = sft_df, aes(x = Power, y = sft_signedR2), size=6) + 
  geom_hline(yintercept = 0.8, col="red") # this line corresponds to using an R^2 cut-off of h
# Mean connectivity as a function of the soft-thresholding power
pMC <- ggplot(data = sft_df, aes(x = Power, y = mean.k, label = powers)) + 
       xlab("Soft Threshold (power)") +
       ylab("Mean Connectivity") +
       ggtitle("Mean Connectivity") +
  theme_classic() +
  theme(text = element_text(size=16)) +
  geom_text(data = sft_df, aes(x = Power, y = mean.k), size=6)

par(mar = c(4, 4, .1, .1))
pSI
pMC
Figure S2a.  Network construction using 10,247 genes of 66 SRA varroa libraries.  Picking soft threshold.Figure S2a.  Network construction using 10,247 genes of 66 SRA varroa libraries.  Picking soft threshold.

Figure S2a. Network construction using 10,247 genes of 66 SRA varroa libraries. Picking soft threshold.

Constructing the gene network and identifying modules is now a simple function call: (Figure S1b)

net = blockwiseModules(for_modules, power = 12,
                       TOMType = "unsigned", minModuleSize = 30,
                       reassignThreshold = 0, mergeCutHeight = 0.25, #0.25 means a correlation of 0.75
                       numericLabels = TRUE, pamRespectsDendro = FALSE,
                       #saveTOMs = TRUE,
                       #saveTOMFileBase = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/Varroa_modulesTOM", 
                       verbose = 3)

# To see how many modules were identified and what the module sizes are, one can use table(net$colors).
table(net$colors)
#saveRDS(net, "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/net.rds")

Based on the analysis of network topology, for the construction of the network we set our threshold for merging of modules to 0.25, minimum number of 30 genes per module, and the power β of 12. This power is the lowest for which the scale-free topology fit index curve flattens out upon reaching a high value, in this case, when Rsq reaches 0.886 (Fig S2a). We then performed hierarchical clustering of the genes based on topological overlap (sharing of network neighborhood) to identify groups of genes who coexpressed across libraries, these are the network modules (fig S2b).

The hierarchical clustering dendrogram (tree) used for the module identification is returned in net$dendrograms[[1]]; The dendrogram can be displayed together with the color assignment using the following code

net <- readRDS("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/net.rds")

# Convert labels to colors for plotting
mergedColors = labels2colors(net$colors)
# Plot the dendrogram and the module colors underneath
plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
                    "Module colors",
                    dendroLabels = FALSE, hang = 0.03,
                    addGuide = TRUE, guideHang = 0.05)
Figure S2b. Network construction using 10,247 genes of 66 SRA varroa libraries. Hierarchical clustering dendrogram using merge cut height of 25%, revealing 15 co-expressed genes modules. Each branch of the dendrogram represents a single gene, and the colored bar below denotes its corresponding module, as annotated in the legend to the right. The dendrogram height is the distance between genes.

Figure S2b. Network construction using 10,247 genes of 66 SRA varroa libraries. Hierarchical clustering dendrogram using merge cut height of 25%, revealing 15 co-expressed genes modules. Each branch of the dendrogram represents a single gene, and the colored bar below denotes its corresponding module, as annotated in the legend to the right. The dendrogram height is the distance between genes.

Save the module assignment and module eigengene information necessary for subsequent analysis:

moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs;
geneTree = net$dendrograms[[1]];
#save(MEs, moduleLabels, moduleColors, geneTree, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/Varroa_modules_networkConstruction-auto.RData")

(2) Figure 2b. Correlating modules to viral load

To test if the varroa modules interact with the different viruses it carries, we correlated the module eigengenes to the viruses’ load (log10TPM). We used Pearson correlation method and adjusted the p-values for multiple comparisons using the Benjamini–Hochberg method to control the false discovery rate (Benjamini and Hochberg 1995) (Fig 2b).

# For correlating varroa modules to viral load, we gonna use the table of 15 viruses saved in chunk "viral correlation", in section "viral correlation matrix", and correlated these to the varroa modules eigengenes found in the previous chunk. 

# First we load the two data:
load("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load_15.rds")
# change the names of the viruses to match their common name in the literature:
viruses_load_15 <- viruses_load_15 %>%
  dplyr::rename("VOV-1" = "VOV_1", "ARV-2"= "ARV_2", "SBV"= "SV", "DWVb"="VDV1/DWVb")

load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/Varroa_modules_networkConstruction-auto.RData")
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/for_modules.rds")

# Define numbers of genes and samples
nGenes = ncol(for_modules);
nSamples = nrow(for_modules)
# Recalculate MEs with color labels 
MEs0 = moduleEigengenes(for_modules, moduleColors)$eigengenes
MEs = orderMEs(MEs0)

# correlate the modules eigengenes (MEs) with the viral load (viruses_load_15)
moduleTraitCor_66 = cor(MEs, viruses_load_15, use = "p") %>%
  as.matrix()
moduleTraitPvalue = corPvalueStudent(moduleTraitCor_66, nSamples)

### Controlling the false discovery rate: Benjamini–Hochberg procedure ###
# using p.adjust function, for all comparisons, 15 modules and 15 viruses (m=225). 

# first make the p-value matrix into a dataframe
moduleTraitPvalue_0 <- as.data.frame(moduleTraitPvalue)

# then "gather" all the p-values, so they will apear in one column
longer_Pvalue <- moduleTraitPvalue_0 %>% 
  rownames_to_column("module") %>%
  gather("virus", "pvalue", -module)

# now calculate the p.adjust for each p-value 
Padjust <- p.adjust(longer_Pvalue$pvalue, method = "fdr")

# and add the column of adjusted pvalues
Padjust <- add_column(longer_Pvalue, Padjust)

# now spread it back
moduleTraitPadjust <- Padjust %>% 
  dplyr::select(-pvalue) %>% 
  group_by(virus) %>%
  pivot_wider(names_from = virus, values_from = Padjust) 
moduleTraitPadjust <- column_to_rownames(moduleTraitPadjust, "module") %>%
  as.matrix()
#  Display correlations and their adjusted p-values
textMatrix = paste(signif(moduleTraitCor_66, 2), "\n(",
                   signif(moduleTraitPadjust, 1), ")", sep = "");
dim(textMatrix) = dim(moduleTraitCor_66)
par(mar = c(6, 8.5, 3, 3));
# Display the correlation values within a heatmap plot
labeledHeatmap(Matrix = moduleTraitCor_66,
               xLabels = names(viruses_load_15),
               yLabels = names(MEs),
               #xLabelsAngle = 90,
               ySymbols = names(MEs),
               colorLabels = FALSE,
               colors = hcl.colors(n = 50, palette = "RdBu", alpha = NULL, rev = FALSE, fixup = TRUE),
               invertColors = TRUE,
               textMatrix = textMatrix,
               setStdMargins = FALSE,
               cex.text = 0.7,
               zlim = c(-1,1),
               main = paste("Varroa Module-viruses relationships"))
Figure 2b. Correlation between viruses’ loads and varroa modules (eigengenes).  Viruses and modules are ordered according to hierarchical clustering; P-values of  the Pearson coefficient are adjusted according to FDR-correction. In each cell, module-virus correlation values are given: Pearson correlation coefficient (up) and adjusted P-value.

Figure 2b. Correlation between viruses’ loads and varroa modules (eigengenes). Viruses and modules are ordered according to hierarchical clustering; P-values of the Pearson coefficient are adjusted according to FDR-correction. In each cell, module-virus correlation values are given: Pearson correlation coefficient (up) and adjusted P-value.

# save the matrices for next analyses
#save(moduleTraitCor_66,moduleTraitPadjust_66, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/moduleTraitCor_66.RData")

Correlating varroa modules eigengenes to their viruses’ loads (transcript per million, TPM), we found significant interactions between specific modules and viruses (Pearson correlation followed by Benjamini-Hochberg FDR-correction, P-adjust < 0.1, Fig 2b).

Module number Module color
MM.0 MM.grey
MM.1 MM.turquoise
MM.2 MM.blue
MM.3 MM.brown
MM.4 MM.yellow
MM.5 MM.green
MM.6 MM.red
MM.7 MM.black
MM.8 MM.pink
MM.9 MM.magenta
MM.10 MM.purple
MM.11 MM.greenyellow
MM.1 MM.tan
MM.13 MM.salmon
MM.14 MM.cyan
MM.15 MM.midnightblue

(3) Identifying important genes

The important genes were identified according to their Module membership (Langfelder and Horvath 2008), and their annotation (based on sequence similarity to homologue genes). A gene Module membership expresses its connection to other genes in the module, and therefore, measures the extent to which this gene represents the overall module. The Module membership is calculated by Pearson correlation of the module eigengene and the gene expression. Genes with high Module membership and relevant annotation are likely to play a role in the vector-virus interaction, and are good candidates for later experimental validation.

Calculating gene Module-membership (MM)

# names (colors) of the modules
modNames = substring(names(MEs), 3)
# virusNames = substring(names(viruses_load_15), 1)

#make a table of the Module-membership ("MM") of each gene (which is its correlation coefficient, pearson)
geneModuleMembership_66 = as.data.frame(cor(for_modules, MEs, use = "p"));
MMPvalue_66 = as.data.frame(corPvalueStudent(as.matrix(geneModuleMembership_66), nSamples));

### Controlling the false discovery rate: Benjamini–Hochberg procedure ###
# using p.adjust function, for all comparisons, 15 modules and 15 viruses (m=225). 

# first make the p-value matrix into a dataframe
MMPvalue_66_0 <- as.data.frame(MMPvalue_66)

# then "gather" all the p-values, so they will appear in one column
longer_Pvalue <- MMPvalue_66_0 %>% 
    rownames_to_column("module") %>%
    gather("virus", "pvalue", -module)

# now calculate the p.adjust for each p-value 
Padjust <- p.adjust(longer_Pvalue$pvalue, method = "fdr")

# and add the column of adjusted pvalues
Padjust <- add_column(longer_Pvalue, Padjust)

# now spread it back
MMPadjust_66 <- Padjust %>% 
    dplyr::select(-pvalue) %>% 
    group_by(virus) %>%
    pivot_wider(names_from = virus, values_from = Padjust)
MMPadjust_66 <- column_to_rownames(MMPadjust_66, "module")  
  
#change the name of the columns to start with "MM" then the module name
names(geneModuleMembership_66) = paste("MM", modNames, sep="");
names(MMPadjust_66) = paste("padj.MM", modNames, sep="");
Identifying genes with high Module-membership in module 10 (the purple module) and adding gene annotations
genePurple = data.frame(
  moduleCol = moduleColors,
  geneModuleMembership_66,
  MMPadjust_66) %>%
  dplyr::select(c(moduleCol, MMpurple, padj.MMpurple)) %>%
  dplyr::filter(moduleCol == "purple") %>%
  mutate(moduleNum = "Module.10") %>%
  rownames_to_column("genes")

# add gene annotation:
# load the annotation file:
annot_varroa <- read_csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/annot_varroa.csv", col_names = TRUE, )

# remove the "LOC" from the gene name
annot_varroa$Locus <- str_replace(annot_varroa$Locus, "LOC", '')
# change the col name to "genes", so it will the same as in the "overlap" table
colnames(annot_varroa)[which(names(annot_varroa) == "Locus")] <- "genes"
head(annot_varroa)
## # A tibble: 6 x 11
##   Name  Accession  Start   Stop Strand GeneID genes `Locus tag` `Protein produc…
##   <chr> <chr>      <dbl>  <dbl> <chr>   <dbl> <chr> <chr>       <chr>           
## 1 Un    NW_01921… 3.38e7 3.39e7 -      1.11e8 1112… -           XP_022672900.1  
## 2 Un    NW_01921… 3.38e7 3.39e7 -      1.11e8 1112… -           XP_022672902.1  
## 3 Un    NW_01921… 3.38e7 3.39e7 -      1.11e8 1112… -           XP_022672903.1  
## 4 Un    NW_01921… 3.38e7 3.39e7 -      1.11e8 1112… -           XP_022672904.1  
## 5 Un    NW_01921… 3.38e7 3.39e7 -      1.11e8 1112… -           XP_022672905.1  
## 6 Un    NW_01921… 3.38e7 3.39e7 -      1.11e8 1112… -           XP_022672908.1  
## # … with 2 more variables: Length <dbl>, Protein Name <chr>
genesModule.10 <- left_join(annot_varroa, genePurple, by = "genes") %>%
  na.omit() %>% 
  dplyr::select("genes", "moduleNum", "MMpurple", "padj.MMpurple", "Accession", "Protein Name") %>%
  dplyr::rename(c(MM = MMpurple, MMpadj = padj.MMpurple)) 
# there are total of 263 matching annotations, as some of the genes have a few isoforms.

# save the final table of the genes in module 10
write_csv(genesModule.10, "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/genesModule.10.csv")
Identifying genes with high Module-membership in module 9
Identifying genes with high Module-membership in module 6
Identifying genes with high Module-membership in module 3

Calculating Gene Significanse (GS)

# save(geneTraitSignificance_66, GSPadjust_66, geneModuleMembership_66, MMPadjust_66, file = "/results/geneTraitANDgeneMM_66.RData")

(4) GO-term enrichment analysis for varroa modules (Tables S2-S10)

Analysis based on Tehcer et al. (2019)

# load the annotation table of Varroa destructor
annot.vd <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/VdesGOready2.csv") 

#Preparing the GO frame
annot.vd2 <- annot.vd %>%
  mutate(evidence = "IEA") %>%
  dplyr::select(go_id = GO.ids, evidence, gene = Gene.id)

#head(annot.vd2)

goFrame.vd <-GOFrame(annot.vd2, organism = "Vd")
goAllFrame.vd <-GOAllFrame(goFrame.vd)
gsc.vd <-GeneSetCollection(goAllFrame.vd, setType = GOCollection())

#Preparing the universe
universe.vd <- as.character(unique(annot.vd2$gene)) # there's a wired thing in the GSEAGOHyperGParams function, sometimes its required the universe to be "character".
#head(universe.vd)

# Preparing the gene set (list of genes in a module) 
# change "black" to the name of the desired module, in the first line: [moduleColors=="black"], and in the final "write.csv(file = "GO_term_enrichment_**salmon**BP.csv")
ME <- names(for_modules)[moduleColors=="black"]
ME_df <- data.frame(gene = ME)
genes.vd <- unique(ME_df$gene)
head(genes.vd)
## [1] "111242800" "111242844" "111242861" "111242884" "111242885" "111242988"
params.vd <- GSEAGOHyperGParams(name = "Vd_GO_enrichment",
                                geneSetCollection = gsc.vd,
                                geneIds = genes.vd,
                                universeGeneIds = universe.vd,
                                ontology = "BP", # change with MF, CC to test all
                                pvalueCutoff = 0.05,
                                conditional = F,
                                testDirection = "over")

over.vd <- hyperGTest(params.vd)
#over.vd
#summary(over.vd)

GO_enrich.vd <- as.data.frame(summary(over.vd)) %>% 
  arrange(Pvalue)

# write.csv(GO_enrich.vd, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_black.csv")

All GO-terms of the significantly interacting modules are also available as csv files, on the github project result folder

Significant GO-terms of the interacting modules

Module 1
GO_term_turquoise <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_turquoise.csv")
GO_term_turquoise %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0043043 0.0000000 5.007628 97.968685 184 242 peptide biosynthetic process
2 GO:0006412 0.0000000 5.036588 96.754197 182 239 translation
3 GO:0043604 0.0000000 4.617744 103.231466 190 255 amide biosynthetic process
4 GO:0006518 0.0000000 4.376512 109.708734 199 271 peptide metabolic process
5 GO:0043603 0.0000000 3.590242 123.068100 211 304 cellular amide metabolic process
6 GO:0034641 0.0000000 1.859933 684.161479 858 1690 cellular nitrogen compound metabolic process
7 GO:1901566 0.0000000 2.429725 208.487078 310 515 organonitrogen compound biosynthetic process
8 GO:0034660 0.0000000 4.251384 70.035465 127 173 ncRNA metabolic process
9 GO:0006396 0.0000000 2.873901 117.400491 188 290 RNA processing
10 GO:0022613 0.0000000 5.417015 46.150538 89 114 ribonucleoprotein complex biogenesis
11 GO:0042254 0.0000000 8.029258 33.196001 69 82 ribosome biogenesis
12 GO:0044237 0.0000000 1.578136 1168.742124 1312 2887 cellular metabolic process
13 GO:0006807 0.0000000 1.569641 1133.521977 1276 2800 nitrogen compound metabolic process
14 GO:0034470 0.0000000 4.565027 50.198830 93 124 ncRNA processing
15 GO:0010467 0.0000000 1.612678 525.468402 640 1298 gene expression
16 GO:0008152 0.0000000 1.563687 1438.358423 1562 3553 metabolic process
17 GO:0071704 0.0000000 1.518342 1272.783248 1400 3144 organic substance metabolic process
18 GO:0044238 0.0000000 1.502527 1209.225052 1336 2987 primary metabolic process
19 GO:0043170 0.0000000 1.488247 1020.574609 1147 2521 macromolecule metabolic process
20 GO:0006399 0.0000000 4.418506 41.292586 76 102 tRNA metabolic process
21 GO:0006725 0.0000000 1.479120 594.694209 696 1469 cellular aromatic compound metabolic process
22 GO:0046483 0.0000000 1.464680 594.289379 693 1468 heterocycle metabolic process
23 GO:1901360 0.0000000 1.443885 610.482551 707 1508 organic cyclic compound metabolic process
24 GO:0006139 0.0000000 1.447993 576.072062 670 1423 nucleobase-containing compound metabolic process
25 GO:0008033 0.0000000 5.133052 25.099415 48 62 tRNA processing
26 GO:0006259 0.0000000 2.128167 92.301075 133 228 DNA metabolic process
27 GO:0044267 0.0000000 1.432762 480.127523 561 1186 cellular protein metabolic process
28 GO:0006974 0.0000000 2.280997 74.083758 110 183 cellular response to DNA damage stimulus
29 GO:0009451 0.0000001 4.072299 27.123562 49 67 RNA modification
30 GO:0016072 0.0000001 4.824656 22.265610 42 55 rRNA metabolic process
31 GO:0006364 0.0000001 5.290417 20.241464 39 50 rRNA processing
32 GO:0033554 0.0000001 1.860501 127.521222 173 315 cellular response to stress
33 GO:0008380 0.0000001 3.150504 37.649123 63 93 RNA splicing
34 GO:0090304 0.0000001 1.405291 504.822109 584 1247 nucleic acid metabolic process
35 GO:0044249 0.0000004 1.365788 573.238257 652 1416 cellular biosynthetic process
36 GO:0009057 0.0000005 1.953867 92.705905 129 229 macromolecule catabolic process
37 GO:0044265 0.0000009 2.063378 75.703075 108 187 cellular macromolecule catabolic process
38 GO:0009058 0.0000012 1.341800 598.742501 675 1479 biosynthetic process
39 GO:0006400 0.0000013 6.687353 13.359366 27 33 tRNA modification
40 GO:1901576 0.0000014 1.342540 583.763818 659 1442 organic substance biosynthetic process
41 GO:0006260 0.0000016 2.937504 33.600830 55 83 DNA replication
42 GO:0030163 0.0000022 2.063498 70.035465 100 173 protein catabolic process
43 GO:0044260 0.0000030 1.300215 806.015092 885 1991 cellular macromolecule metabolic process
44 GO:0044257 0.0000043 2.236931 53.437465 79 132 cellular protein catabolic process
45 GO:0051603 0.0000043 2.236931 53.437465 79 132 proteolysis involved in cellular protein catabolic process
46 GO:0019538 0.0000054 1.321495 570.809281 641 1410 protein metabolic process
47 GO:0006281 0.0000065 2.220796 52.222977 77 129 DNA repair
48 GO:1901565 0.0000080 1.819851 91.086587 123 225 organonitrogen compound catabolic process
49 GO:0000398 0.0000106 2.812094 30.362196 49 75 mRNA splicing, via spliceosome
50 GO:0000375 0.0000106 2.812094 30.362196 49 75 RNA splicing, via transesterification reactions
51 GO:0000377 0.0000106 2.812094 30.362196 49 75 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
52 GO:0016071 0.0000120 2.032743 61.938879 88 153 mRNA metabolic process
53 GO:0034645 0.0000123 1.330952 467.982645 531 1156 cellular macromolecule biosynthetic process
54 GO:1901564 0.0000126 1.286134 705.617431 777 1743 organonitrogen compound metabolic process
55 GO:0140053 0.0000133 12.588304 7.691756 17 19 mitochondrial gene expression
56 GO:0006520 0.0000154 2.334716 42.507074 64 105 cellular amino acid metabolic process
57 GO:0009056 0.0000172 1.543975 164.765516 205 407 catabolic process
58 GO:0009059 0.0000177 1.322441 472.030938 534 1166 macromolecule biosynthetic process
59 GO:1901575 0.0000214 1.588293 140.070930 177 346 organic substance catabolic process
60 GO:0043632 0.0000232 2.196826 46.960196 69 116 modification-dependent macromolecule catabolic process
61 GO:0051186 0.0000234 2.227246 45.340879 67 112 cofactor metabolic process
62 GO:0044248 0.0000263 1.568512 144.928881 182 358 cellular catabolic process
63 GO:0022618 0.0000291 3.658540 18.217318 32 45 ribonucleoprotein complex assembly
64 GO:0043038 0.0000323 4.157696 15.383513 28 38 amino acid activation
65 GO:0043039 0.0000323 4.157696 15.383513 28 38 tRNA aminoacylation
66 GO:0006418 0.0000323 4.157696 15.383513 28 38 tRNA aminoacylation for protein translation
67 GO:0019941 0.0000351 2.178127 45.745708 67 113 modification-dependent protein catabolic process
68 GO:0006511 0.0000351 2.178127 45.745708 67 113 ubiquitin-dependent protein catabolic process
69 GO:0006397 0.0000356 2.208455 44.126391 65 109 mRNA processing
70 GO:0071826 0.0000588 3.396135 18.622147 32 46 ribonucleoprotein complex subunit organization
71 GO:0032543 0.0000658 11.096903 6.882098 15 17 mitochondrial translation
72 GO:0006457 0.0000843 2.278880 36.839464 55 91 protein folding
73 GO:0006790 0.0001323 2.971591 20.646293 34 51 sulfur compound metabolic process
74 GO:0042273 0.0001447 10.352251 6.477268 14 16 ribosomal large subunit biogenesis
75 GO:0001522 0.0001552 17.735708 5.262781 12 13 pseudouridine synthesis
76 GO:0000278 0.0003636 1.853689 52.627806 72 130 mitotic cell cycle
77 GO:0044271 0.0003786 1.261487 449.360498 499 1110 cellular nitrogen compound biosynthetic process
78 GO:0009987 0.0004146 1.248263 1621.341256 1673 4005 cellular process
79 GO:0043436 0.0004773 1.620858 82.585173 106 204 oxoacid metabolic process
80 GO:0006082 0.0004773 1.620858 82.585173 106 204 organic acid metabolic process
81 GO:0006779 0.0007158 Inf 3.238634 8 8 porphyrin-containing compound biosynthetic process
82 GO:0006415 0.0008130 14.765918 4.453122 10 11 translational termination
83 GO:0006778 0.0008130 14.765918 4.453122 10 11 porphyrin-containing compound metabolic process
84 GO:0019752 0.0008225 1.588718 81.775514 104 202 carboxylic acid metabolic process
85 GO:0006950 0.0009121 1.345459 206.462931 240 510 response to stress
86 GO:0000086 0.0010573 6.403500 6.477268 13 16 G2/M transition of mitotic cell cycle
87 GO:0007049 0.0010597 1.488883 106.470100 131 263 cell cycle
88 GO:0045184 0.0010800 1.469529 113.757027 139 281 establishment of protein localization
89 GO:0007005 0.0012181 1.923275 38.053952 53 94 mitochondrion organization
90 GO:0071840 0.0012356 1.241832 408.877570 452 1010 cellular component organization or biogenesis
91 GO:0006611 0.0014467 5.172842 7.286927 14 18 protein export from nucleus
92 GO:0042255 0.0014628 8.122482 5.262781 11 13 ribosome assembly
93 GO:0044272 0.0018290 4.434538 8.096585 15 20 sulfur compound biosynthetic process
94 GO:0000387 0.0018405 13.283107 4.048293 9 10 spliceosomal snRNP assembly
95 GO:0090150 0.0019263 3.108000 12.549708 21 31 establishment of protein localization to membrane
96 GO:0033013 0.0021524 5.908154 6.072439 12 15 tetrapyrrole metabolic process
97 GO:0006261 0.0022931 2.733560 14.978683 24 37 DNA-dependent DNA replication
98 GO:0006886 0.0023134 1.524627 80.156197 100 198 intracellular protein transport
99 GO:0016070 0.0023557 1.218765 434.786644 476 1074 RNA metabolic process
100 GO:1903047 0.0024989 1.755582 44.126391 59 109 mitotic cell cycle process
101 GO:0007346 0.0025679 2.192194 23.075269 34 57 regulation of mitotic cell cycle
102 GO:0072527 0.0028261 4.801102 6.882098 13 17 pyrimidine-containing compound metabolic process
103 GO:0072594 0.0028737 1.897804 33.196001 46 82 establishment of protein localization to organelle
104 GO:0042278 0.0030960 7.380618 4.857951 10 12 purine nucleoside metabolic process
105 GO:0042886 0.0034006 1.419737 107.279758 129 265 amide transport
106 GO:0006605 0.0034637 1.995221 27.528391 39 68 protein targeting
107 GO:0015031 0.0035530 1.418933 106.470100 128 263 protein transport
108 GO:0045454 0.0039790 2.406073 17.002830 26 42 cell redox homeostasis
109 GO:0048364 0.0041292 11.801684 3.643464 8 9 root development
110 GO:0031145 0.0041292 11.801684 3.643464 8 9 anaphase-promoting complex-dependent catabolic process
111 GO:0022622 0.0041292 11.801684 3.643464 8 9 root system development
112 GO:0015833 0.0041983 1.408034 106.874929 128 264 peptide transport
113 GO:0042274 0.0043216 5.413271 5.667610 11 14 ribosomal small subunit biogenesis
114 GO:0097300 0.0043835 Inf 2.428976 6 6 programmed necrotic cell death
115 GO:1901990 0.0049208 3.141087 10.120732 17 25 regulation of mitotic cell cycle phase transition
116 GO:0071426 0.0054379 4.429710 6.477268 12 16 ribonucleoprotein complex export from nucleus
117 GO:0071166 0.0054379 4.429710 6.477268 12 16 ribonucleoprotein complex localization
118 GO:0006289 0.0054379 4.429710 6.477268 12 16 nucleotide-excision repair
119 GO:0044281 0.0054737 1.293010 182.982833 209 452 small molecule metabolic process
120 GO:1903827 0.0056830 2.037447 23.075269 33 57 regulation of cellular protein localization
121 GO:0033365 0.0060184 1.614970 48.984343 63 121 protein localization to organelle
122 GO:1903829 0.0060863 2.503404 14.169025 22 35 positive regulation of cellular protein localization
123 GO:0044839 0.0064124 3.839662 7.286927 13 18 cell cycle G2/M phase transition
124 GO:0000413 0.0064124 3.839662 7.286927 13 18 protein peptidyl-prolyl isomerization
125 GO:0031570 0.0064124 3.839662 7.286927 13 18 DNA integrity checkpoint
126 GO:0018208 0.0064124 3.839662 7.286927 13 18 peptidyl-proline modification
127 GO:0006220 0.0064646 6.639448 4.453122 9 11 pyrimidine nucleotide metabolic process
128 GO:0044085 0.0069782 1.275013 192.293907 218 475 cellular component biogenesis
129 GO:0051188 0.0070292 1.877767 27.528391 38 68 cofactor biosynthetic process
130 GO:0006414 0.0072378 3.446373 8.096585 14 20 translational elongation
131 GO:0043161 0.0079183 1.937391 24.289757 34 60 proteasome-mediated ubiquitin-dependent protein catabolic process
132 GO:0042180 0.0079195 3.165516 8.906244 15 22 cellular ketone metabolic process
133 GO:0048193 0.0081380 1.955324 23.480098 33 58 Golgi vesicle transport
134 GO:0000077 0.0085402 4.918851 5.262781 10 13 DNA damage checkpoint
135 GO:0033014 0.0085402 4.918851 5.262781 10 13 tetrapyrrole biosynthetic process
136 GO:0031398 0.0088998 2.791190 10.525561 17 26 positive regulation of protein ubiquitination
137 GO:1903322 0.0088998 2.791190 10.525561 17 26 positive regulation of protein modification by small protein conjugation or removal
138 GO:0070265 0.0091623 10.321646 3.238634 7 8 necrotic cell death
139 GO:0006739 0.0091623 10.321646 3.238634 7 8 NADP metabolic process
140 GO:1901987 0.0092262 2.660244 11.335220 18 28 regulation of cell cycle phase transition
141 GO:0099402 0.0102868 4.058665 6.072439 11 15 plant organ development
142 GO:0042168 0.0108431 Inf 2.024146 5 5 heme metabolic process
143 GO:0010053 0.0108431 Inf 2.024146 5 5 root epidermal cell differentiation
144 GO:0017004 0.0108431 Inf 2.024146 5 5 cytochrome complex assembly
145 GO:0010015 0.0108431 Inf 2.024146 5 5 root morphogenesis
146 GO:0007398 0.0108431 Inf 2.024146 5 5 ectoderm development
147 GO:0000394 0.0108431 Inf 2.024146 5 5 RNA splicing, via endonucleolytic cleavage and ligation
148 GO:0000463 0.0108431 Inf 2.024146 5 5 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
149 GO:0000470 0.0108431 Inf 2.024146 5 5 maturation of LSU-rRNA
150 GO:0097039 0.0108431 Inf 2.024146 5 5 protein linear polyubiquitination
151 GO:0070266 0.0108431 Inf 2.024146 5 5 necroptotic process
152 GO:0007220 0.0108431 Inf 2.024146 5 5 Notch receptor processing
153 GO:0033146 0.0108431 Inf 2.024146 5 5 regulation of intracellular estrogen receptor signaling pathway
154 GO:0009067 0.0108431 Inf 2.024146 5 5 aspartate family amino acid biosynthetic process
155 GO:0010992 0.0108431 Inf 2.024146 5 5 ubiquitin recycling
156 GO:0010994 0.0108431 Inf 2.024146 5 5 free ubiquitin chain polymerization
157 GO:0090558 0.0108431 Inf 2.024146 5 5 plant epidermis development
158 GO:0090627 0.0108431 Inf 2.024146 5 5 plant epidermal cell differentiation
159 GO:1901068 0.0108431 Inf 2.024146 5 5 guanosine-containing compound metabolic process
160 GO:0009226 0.0108431 Inf 2.024146 5 5 nucleotide-sugar biosynthetic process
161 GO:0009733 0.0108431 Inf 2.024146 5 5 response to auxin
162 GO:0006098 0.0108431 Inf 2.024146 5 5 pentose-phosphate shunt
163 GO:0030520 0.0108431 Inf 2.024146 5 5 intracellular estrogen receptor signaling pathway
164 GO:0019682 0.0108431 Inf 2.024146 5 5 glyceraldehyde-3-phosphate metabolic process
165 GO:0006388 0.0108431 Inf 2.024146 5 5 tRNA splicing, via endonucleolytic cleavage and ligation
166 GO:0051156 0.0108431 Inf 2.024146 5 5 glucose 6-phosphate metabolic process
167 GO:1901570 0.0108431 Inf 2.024146 5 5 fatty acid derivative biosynthetic process
168 GO:0006783 0.0108431 Inf 2.024146 5 5 heme biosynthetic process
169 GO:0006544 0.0108431 Inf 2.024146 5 5 glycine metabolic process
170 GO:0016073 0.0117062 3.542643 6.882098 12 17 snRNA metabolic process
171 GO:0051028 0.0117062 3.542643 6.882098 12 17 mRNA transport
172 GO:0044770 0.0125040 1.930632 21.455952 30 53 cell cycle phase transition
173 GO:0006633 0.0128275 3.198703 7.691756 13 19 fatty acid biosynthetic process
174 GO:0010498 0.0129994 1.759280 28.338049 38 70 proteasomal protein catabolic process
175 GO:0051187 0.0132838 5.898971 4.048293 8 10 cofactor catabolic process
176 GO:1901661 0.0132838 5.898971 4.048293 8 10 quinone metabolic process
177 GO:0090501 0.0136883 2.953096 8.501415 14 21 RNA phosphodiester bond hydrolysis
178 GO:0009267 0.0136883 2.953096 8.501415 14 21 cellular response to starvation
179 GO:0043933 0.0147306 1.324910 109.303905 127 270 protein-containing complex subunit organization
180 GO:0051168 0.0147767 2.625769 10.120732 16 25 nuclear export
181 GO:0044283 0.0148824 1.537202 46.150538 58 114 small molecule biosynthetic process
182 GO:0000075 0.0152319 2.417635 11.740049 18 29 cell cycle checkpoint
183 GO:0019725 0.0155556 1.574099 40.887757 52 101 cellular homeostasis
184 GO:0006732 0.0165605 1.699084 29.552537 39 73 coenzyme metabolic process
185 GO:0048229 0.0165701 4.424895 4.857951 9 12 gametophyte development
186 GO:0010389 0.0165701 4.424895 4.857951 9 12 regulation of G2/M transition of mitotic cell cycle
187 GO:0033143 0.0165701 4.424895 4.857951 9 12 regulation of intracellular steroid hormone receptor signaling pathway
188 GO:0072528 0.0165701 4.424895 4.857951 9 12 pyrimidine-containing compound biosynthetic process
189 GO:0008104 0.0174754 1.259311 155.859272 176 385 protein localization
190 GO:0009119 0.0190866 3.687968 5.667610 10 14 ribonucleoside metabolic process
191 GO:0071705 0.0193330 1.281794 127.926052 146 316 nitrogen compound transport
192 GO:1902914 0.0200549 8.842991 2.833805 6 7 regulation of protein polyubiquitination
193 GO:1902916 0.0200549 8.842991 2.833805 6 7 positive regulation of protein polyubiquitination
194 GO:1905392 0.0200549 8.842991 2.833805 6 7 plant organ morphogenesis
195 GO:0006613 0.0200549 8.842991 2.833805 6 7 cotranslational protein targeting to membrane
196 GO:0006614 0.0200549 8.842991 2.833805 6 7 SRP-dependent cotranslational protein targeting to membrane
197 GO:0018193 0.0202104 1.426657 60.319562 73 149 peptidyl-amino acid modification
198 GO:0006913 0.0202974 1.735306 25.504244 34 63 nucleocytoplasmic transport
199 GO:0030518 0.0222937 2.951265 7.286927 12 18 intracellular steroid hormone receptor signaling pathway
200 GO:0008593 0.0222937 2.951265 7.286927 12 18 regulation of Notch signaling pathway
201 GO:0006403 0.0231665 2.110603 13.764195 20 34 RNA localization
202 GO:0006733 0.0231665 2.110603 13.764195 20 34 oxidoreduction coenzyme metabolic process
203 GO:0031669 0.0237836 2.583138 8.906244 14 22 cellular response to nutrient levels
204 GO:0006405 0.0237836 2.583138 8.906244 14 22 RNA export from nucleus
205 GO:0045787 0.0237836 2.583138 8.906244 14 22 positive regulation of cell cycle
206 GO:0006413 0.0241799 2.362441 10.525561 16 26 translational initiation
207 GO:0034613 0.0254375 1.271281 122.258442 139 302 cellular protein localization
208 GO:0046907 0.0255743 1.255536 136.427467 154 337 intracellular transport
209 GO:0000079 0.0267781 5.159186 3.643464 7 9 regulation of cyclin-dependent protein serine/threonine kinase activity
210 GO:0046128 0.0267781 5.159186 3.643464 7 9 purine ribonucleoside metabolic process
211 GO:0097352 0.0267781 5.159186 3.643464 7 9 autophagosome maturation
212 GO:0009225 0.0267781 5.159186 3.643464 7 9 nucleotide-sugar metabolic process
213 GO:0045292 0.0267781 5.159186 3.643464 7 9 mRNA cis splicing, via spliceosome
214 GO:0006749 0.0267781 5.159186 3.643464 7 9 glutathione metabolic process
215 GO:1901659 0.0267781 5.159186 3.643464 7 9 glycosyl compound biosynthetic process
216 GO:1990592 0.0268142 Inf 1.619317 4 4 protein K69-linked ufmylation
217 GO:1990564 0.0268142 Inf 1.619317 4 4 protein polyufmylation
218 GO:0048132 0.0268142 Inf 1.619317 4 4 female germ-line stem cell asymmetric division
219 GO:0071569 0.0268142 Inf 1.619317 4 4 protein ufmylation
220 GO:0070129 0.0268142 Inf 1.619317 4 4 regulation of mitochondrial translation
221 GO:0010421 0.0268142 Inf 1.619317 4 4 hydrogen peroxide-mediated programmed cell death
222 GO:0090351 0.0268142 Inf 1.619317 4 4 seedling development
223 GO:0097468 0.0268142 Inf 1.619317 4 4 programmed cell death in response to reactive oxygen species
224 GO:0010668 0.0268142 Inf 1.619317 4 4 ectodermal cell differentiation
225 GO:0110116 0.0268142 Inf 1.619317 4 4 regulation of compound eye photoreceptor cell differentiation
226 GO:0010939 0.0268142 Inf 1.619317 4 4 regulation of necrotic cell death
227 GO:0030447 0.0268142 Inf 1.619317 4 4 filamentous growth
228 GO:0009219 0.0268142 Inf 1.619317 4 4 pyrimidine deoxyribonucleotide metabolic process
229 GO:0002756 0.0268142 Inf 1.619317 4 4 MyD88-independent toll-like receptor signaling pathway
230 GO:0008334 0.0268142 Inf 1.619317 4 4 histone mRNA metabolic process
231 GO:0006465 0.0268142 Inf 1.619317 4 4 signal peptide processing
232 GO:0035519 0.0268142 Inf 1.619317 4 4 protein K29-linked ubiquitination
233 GO:0006284 0.0268142 Inf 1.619317 4 4 base-excision repair
234 GO:0044282 0.0276599 1.830278 19.026976 26 47 small molecule catabolic process
235 GO:0044772 0.0276599 1.830278 19.026976 26 47 mitotic cell cycle phase transition
236 GO:0006839 0.0291935 1.690499 24.289757 32 60 mitochondrial transport
237 GO:0000209 0.0297177 1.866759 17.407659 24 43 protein polyubiquitination
238 GO:0070727 0.0309441 1.256652 123.877759 140 306 cellular macromolecule localization
239 GO:0002097 0.0314684 3.931400 4.453122 8 11 tRNA wobble base modification
240 GO:0002098 0.0314684 3.931400 4.453122 8 11 tRNA wobble uridine modification
241 GO:0031163 0.0314684 3.931400 4.453122 8 11 metallo-sulfur cluster assembly
242 GO:0070979 0.0314684 3.931400 4.453122 8 11 protein K11-linked ubiquitination
243 GO:0016226 0.0314684 3.931400 4.453122 8 11 iron-sulfur cluster assembly
244 GO:0031396 0.0328466 1.938794 14.978683 21 37 regulation of protein ubiquitination
245 GO:0072330 0.0328466 1.938794 14.978683 21 37 monocarboxylic acid biosynthetic process
246 GO:0006401 0.0331593 1.715069 21.860781 29 54 RNA catabolic process
247 GO:0071427 0.0346374 3.317618 5.262781 9 13 mRNA-containing ribonucleoprotein complex export from nucleus
248 GO:0000154 0.0346374 3.317618 5.262781 9 13 rRNA modification
249 GO:0070972 0.0346374 3.317618 5.262781 9 13 protein localization to endoplasmic reticulum
250 GO:0006406 0.0346374 3.317618 5.262781 9 13 mRNA export from nucleus
251 GO:0051169 0.0348084 1.622312 26.313903 34 65 nuclear transport
252 GO:0033157 0.0357974 2.044390 12.549708 18 31 regulation of intracellular protein transport
253 GO:0051604 0.0357974 2.044390 12.549708 18 31 protein maturation
254 GO:0022402 0.0363951 1.314003 79.346538 92 196 cell cycle process
255 GO:0000956 0.0366651 2.091397 11.740049 17 29 nuclear-transcribed mRNA catabolic process
256 GO:0071456 0.0366863 2.949438 6.072439 10 15 cellular response to hypoxia
257 GO:0036294 0.0366863 2.949438 6.072439 10 15 cellular response to decreased oxygen levels
258 GO:0050657 0.0374310 2.146991 10.930390 16 27 nucleic acid transport
259 GO:0050658 0.0374310 2.146991 10.930390 16 27 RNA transport
260 GO:0032388 0.0374310 2.146991 10.930390 16 27 positive regulation of intracellular transport
261 GO:0051236 0.0374310 2.146991 10.930390 16 27 establishment of RNA localization
262 GO:0006888 0.0374310 2.146991 10.930390 16 27 ER to Golgi vesicle-mediated transport
263 GO:0032386 0.0375962 1.746527 19.431805 26 48 regulation of intracellular transport
264 GO:0090068 0.0379097 2.704059 6.882098 11 17 positive regulation of cell cycle process
265 GO:0031668 0.0384947 2.295393 9.311073 14 23 cellular response to extracellular stimulus
266 GO:0046394 0.0398556 1.636896 23.884927 31 59 carboxylic acid biosynthetic process
267 GO:0016053 0.0398556 1.636896 23.884927 31 59 organic acid biosynthetic process
268 GO:0034622 0.0412865 1.308288 76.917563 89 190 cellular protein-containing complex assembly
269 GO:0055086 0.0425111 1.314163 73.274099 85 181 nucleobase-containing small molecule metabolic process
270 GO:0071616 0.0431411 7.365717 2.428976 5 6 acyl-CoA biosynthetic process
271 GO:0097354 0.0431411 7.365717 2.428976 5 6 prenylation
272 GO:0009066 0.0431411 7.365717 2.428976 5 6 aspartate family amino acid metabolic process
273 GO:0009081 0.0431411 7.365717 2.428976 5 6 branched-chain amino acid metabolic process
274 GO:0035384 0.0431411 7.365717 2.428976 5 6 thioester biosynthetic process
275 GO:0018342 0.0431411 7.365717 2.428976 5 6 protein prenylation
276 GO:0006378 0.0431411 7.365717 2.428976 5 6 mRNA polyadenylation
277 GO:0051205 0.0431411 7.365717 2.428976 5 6 protein insertion into membrane
278 GO:0044774 0.0431411 7.365717 2.428976 5 6 mitotic DNA integrity checkpoint
279 GO:0070585 0.0460141 1.824166 15.383513 21 38 protein localization to mitochondrion
280 GO:0072655 0.0460141 1.824166 15.383513 21 38 establishment of protein localization to mitochondrion
281 GO:0006626 0.0478263 1.845602 14.573854 20 36 protein targeting to mitochondrion
Module 3
GO_term_brown <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_brown.csv")
GO_term_brown %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0006468 0.0000000 2.525758 37.2090172 76 383 protein phosphorylation
2 GO:0016310 0.0000000 2.157007 44.3010753 80 456 phosphorylation
3 GO:0036211 0.0000006 1.752425 84.0360309 125 865 protein modification process
4 GO:0006464 0.0000006 1.752425 84.0360309 125 865 cellular protein modification process
5 GO:0050766 0.0000021 14.169961 1.4572722 9 15 positive regulation of phagocytosis
6 GO:0006793 0.0000021 1.762184 70.6291266 107 727 phosphorus metabolic process
7 GO:0006796 0.0000027 1.754438 70.1433692 106 722 phosphate-containing compound metabolic process
8 GO:0021549 0.0000030 8.682870 2.2344841 11 23 cerebellum development
9 GO:0022037 0.0000030 8.682870 2.2344841 11 23 metencephalon development
10 GO:0048026 0.0000062 15.087968 1.2629693 8 13 positive regulation of mRNA splicing, via spliceosome
11 GO:0050685 0.0000062 15.087968 1.2629693 8 13 positive regulation of mRNA processing
12 GO:0033120 0.0000062 15.087968 1.2629693 8 13 positive regulation of RNA splicing
13 GO:0042026 0.0000082 7.439342 2.4287870 11 25 protein refolding
14 GO:0061077 0.0000105 6.319417 2.9145444 12 30 chaperone-mediated protein folding
15 GO:0007186 0.0000128 2.767897 12.6296925 29 130 G protein-coupled receptor signaling pathway
16 GO:0030902 0.0000130 6.941931 2.5259385 11 26 hindbrain development
17 GO:0048488 0.0000133 12.570677 1.3601207 8 14 synaptic vesicle endocytosis
18 GO:0140238 0.0000133 12.570677 1.3601207 8 14 presynaptic endocytosis
19 GO:0043412 0.0000154 1.609085 90.9337861 127 936 macromolecule modification
20 GO:0061740 0.0000183 16.473425 1.0686663 7 11 protein targeting to lysosome involved in chaperone-mediated autophagy
21 GO:0071211 0.0000183 16.473425 1.0686663 7 11 protein targeting to vacuole involved in autophagy
22 GO:0090083 0.0000183 16.473425 1.0686663 7 11 regulation of inclusion body assembly
23 GO:0090084 0.0000183 16.473425 1.0686663 7 11 negative regulation of inclusion body assembly
24 GO:0061462 0.0000183 16.473425 1.0686663 7 11 protein localization to lysosome
25 GO:0006622 0.0000183 16.473425 1.0686663 7 11 protein targeting to lysosome
26 GO:0034605 0.0000244 7.270373 2.2344841 10 23 cellular response to heat
27 GO:0010662 0.0000261 10.772612 1.4572722 8 15 regulation of striated muscle cell apoptotic process
28 GO:0010664 0.0000261 10.772612 1.4572722 8 15 negative regulation of striated muscle cell apoptotic process
29 GO:0010665 0.0000261 10.772612 1.4572722 8 15 regulation of cardiac muscle cell apoptotic process
30 GO:0010667 0.0000261 10.772612 1.4572722 8 15 negative regulation of cardiac muscle cell apoptotic process
31 GO:0010656 0.0000261 10.772612 1.4572722 8 15 negative regulation of muscle cell apoptotic process
32 GO:0010658 0.0000261 10.772612 1.4572722 8 15 striated muscle cell apoptotic process
33 GO:0010659 0.0000261 10.772612 1.4572722 8 15 cardiac muscle cell apoptotic process
34 GO:0019538 0.0000382 1.494413 136.9835880 176 1410 protein metabolic process
35 GO:0044849 0.0000403 13.175984 1.1658178 7 12 estrous cycle
36 GO:0061741 0.0000403 13.175984 1.1658178 7 12 chaperone-mediated protein transport involved in chaperone-mediated autophagy
37 GO:0061738 0.0000403 13.175984 1.1658178 7 12 late endosomal microautophagy
38 GO:1990832 0.0000403 13.175984 1.1658178 7 12 slow axonal transport
39 GO:1990834 0.0000403 13.175984 1.1658178 7 12 response to odorant
40 GO:0061684 0.0000403 13.175984 1.1658178 7 12 chaperone-mediated autophagy
41 GO:1904764 0.0000403 13.175984 1.1658178 7 12 chaperone-mediated autophagy translocation complex disassembly
42 GO:0010045 0.0000403 13.175984 1.1658178 7 12 response to nickel cation
43 GO:1904592 0.0000403 13.175984 1.1658178 7 12 positive regulation of protein refolding
44 GO:0070841 0.0000403 13.175984 1.1658178 7 12 inclusion body assembly
45 GO:0001913 0.0000403 13.175984 1.1658178 7 12 T cell mediated cytotoxicity
46 GO:0001914 0.0000403 13.175984 1.1658178 7 12 regulation of T cell mediated cytotoxicity
47 GO:0001916 0.0000403 13.175984 1.1658178 7 12 positive regulation of T cell mediated cytotoxicity
48 GO:0097212 0.0000403 13.175984 1.1658178 7 12 lysosomal membrane organization
49 GO:0097213 0.0000403 13.175984 1.1658178 7 12 regulation of lysosomal membrane permeability
50 GO:0097214 0.0000403 13.175984 1.1658178 7 12 positive regulation of lysosomal membrane permeability
51 GO:0072318 0.0000403 13.175984 1.1658178 7 12 clathrin coat disassembly
52 GO:0072319 0.0000403 13.175984 1.1658178 7 12 vesicle uncoating
53 GO:0002456 0.0000403 13.175984 1.1658178 7 12 T cell mediated immunity
54 GO:1903334 0.0000403 13.175984 1.1658178 7 12 positive regulation of protein folding
55 GO:0002711 0.0000403 13.175984 1.1658178 7 12 positive regulation of T cell mediated immunity
56 GO:0002709 0.0000403 13.175984 1.1658178 7 12 regulation of T cell mediated immunity
57 GO:0016191 0.0000403 13.175984 1.1658178 7 12 synaptic vesicle uncoating
58 GO:0006623 0.0000403 13.175984 1.1658178 7 12 protein targeting to vacuole
59 GO:0010660 0.0000478 9.424063 1.5544237 8 16 regulation of muscle cell apoptotic process
60 GO:0010657 0.0000478 9.424063 1.5544237 8 16 muscle cell apoptotic process
61 GO:0045807 0.0000583 6.298350 2.4287870 10 25 positive regulation of endocytosis
62 GO:0050764 0.0000726 7.076087 2.0401811 9 21 regulation of phagocytosis
63 GO:0006458 0.0000726 7.076087 2.0401811 9 21 ‘de novo’ protein folding
64 GO:0009408 0.0000790 3.850541 5.0518770 15 52 response to heat
65 GO:1905710 0.0000800 10.977690 1.2629693 7 13 positive regulation of membrane permeability
66 GO:0071276 0.0000800 10.977690 1.2629693 7 13 cellular response to cadmium ion
67 GO:0001912 0.0000800 10.977690 1.2629693 7 13 positive regulation of leukocyte mediated cytotoxicity
68 GO:0002460 0.0000800 10.977690 1.2629693 7 13 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
69 GO:0002250 0.0000800 10.977690 1.2629693 7 13 adaptive immune response
70 GO:0002821 0.0000800 10.977690 1.2629693 7 13 positive regulation of adaptive immune response
71 GO:0002822 0.0000800 10.977690 1.2629693 7 13 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
72 GO:0002824 0.0000800 10.977690 1.2629693 7 13 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
73 GO:0002819 0.0000800 10.977690 1.2629693 7 13 regulation of adaptive immune response
74 GO:0061083 0.0000800 10.977690 1.2629693 7 13 regulation of protein refolding
75 GO:0036465 0.0000827 8.375192 1.6515752 8 17 synaptic vesicle recycling
76 GO:1903313 0.0000827 8.375192 1.6515752 8 17 positive regulation of mRNA metabolic process
77 GO:1903332 0.0000827 8.375192 1.6515752 8 17 regulation of protein folding
78 GO:0035821 0.0000827 8.375192 1.6515752 8 17 modification of morphology or physiology of other organism
79 GO:0051817 0.0000827 8.375192 1.6515752 8 17 modification of morphology or physiology of other organism involved in symbiotic interaction
80 GO:0051261 0.0000867 5.903465 2.5259385 10 26 protein depolymerization
81 GO:0002443 0.0001258 5.555038 2.6230900 10 27 leukocyte mediated immunity
82 GO:0032570 0.0001363 7.536095 1.7487267 8 18 response to progesterone
83 GO:1903202 0.0001363 7.536095 1.7487267 8 18 negative regulation of oxidative stress-induced cell death
84 GO:0044829 0.0001466 9.407480 1.3601207 7 14 positive regulation by host of viral genome replication
85 GO:0061635 0.0001466 9.407480 1.3601207 7 14 regulation of protein complex stability
86 GO:2001039 0.0001466 9.407480 1.3601207 7 14 negative regulation of cellular response to drug
87 GO:0001910 0.0001466 9.407480 1.3601207 7 14 regulation of leukocyte mediated cytotoxicity
88 GO:0001909 0.0001466 9.407480 1.3601207 7 14 leukocyte mediated cytotoxicity
89 GO:0031343 0.0001466 9.407480 1.3601207 7 14 positive regulation of cell killing
90 GO:0007608 0.0001466 9.407480 1.3601207 7 14 sensory perception of smell
91 GO:1901032 0.0001466 9.407480 1.3601207 7 14 negative regulation of response to reactive oxygen species
92 GO:0002705 0.0001466 9.407480 1.3601207 7 14 positive regulation of leukocyte mediated immunity
93 GO:0002708 0.0001466 9.407480 1.3601207 7 14 positive regulation of lymphocyte mediated immunity
94 GO:1903206 0.0001466 9.407480 1.3601207 7 14 negative regulation of hydrogen peroxide-induced cell death
95 GO:0032879 0.0001844 1.948133 25.5508395 44 263 regulation of localization
96 GO:0048024 0.0002157 6.849561 1.8458781 8 19 regulation of mRNA splicing, via spliceosome
97 GO:1903201 0.0002157 6.849561 1.8458781 8 19 regulation of oxidative stress-induced cell death
98 GO:0032355 0.0002157 6.849561 1.8458781 8 19 response to estradiol
99 GO:0009266 0.0002458 3.388571 5.5376344 15 57 response to temperature stimulus
100 GO:0044827 0.0002520 8.229823 1.4572722 7 15 modulation by host of viral genome replication
101 GO:0042698 0.0002520 8.229823 1.4572722 7 15 ovulation cycle
102 GO:2001024 0.0002520 8.229823 1.4572722 7 15 negative regulation of response to drug
103 GO:2001038 0.0002520 8.229823 1.4572722 7 15 regulation of cellular response to drug
104 GO:0001906 0.0002520 8.229823 1.4572722 7 15 cell killing
105 GO:0031341 0.0002520 8.229823 1.4572722 7 15 regulation of cell killing
106 GO:0090559 0.0002520 8.229823 1.4572722 7 15 regulation of membrane permeability
107 GO:0002449 0.0002520 8.229823 1.4572722 7 15 lymphocyte mediated immunity
108 GO:0002703 0.0002520 8.229823 1.4572722 7 15 regulation of leukocyte mediated immunity
109 GO:0002706 0.0002520 8.229823 1.4572722 7 15 regulation of lymphocyte mediated immunity
110 GO:0045070 0.0002520 8.229823 1.4572722 7 15 positive regulation of viral genome replication
111 GO:1903205 0.0002520 8.229823 1.4572722 7 15 regulation of hydrogen peroxide-induced cell death
112 GO:0072665 0.0002520 8.229823 1.4572722 7 15 protein localization to vacuole
113 GO:0072666 0.0002520 8.229823 1.4572722 7 15 establishment of protein localization to vacuole
114 GO:0044794 0.0002520 8.229823 1.4572722 7 15 positive regulation by host of viral process
115 GO:0044788 0.0002520 8.229823 1.4572722 7 15 modulation by host of viral process
116 GO:0050684 0.0003292 6.277449 1.9430296 8 20 regulation of mRNA processing
117 GO:1900408 0.0003292 6.277449 1.9430296 8 20 negative regulation of cellular response to oxidative stress
118 GO:0006457 0.0003505 2.683170 8.8407848 20 91 protein folding
119 GO:0034504 0.0003524 3.913347 3.9832107 12 41 protein localization to nucleus
120 GO:0042542 0.0003537 5.302619 2.4287870 9 25 response to hydrogen peroxide
121 GO:0090169 0.0003707 15.630719 0.7772118 5 8 regulation of spindle assembly
122 GO:1901673 0.0003707 15.630719 0.7772118 5 8 regulation of mitotic spindle assembly
123 GO:0006508 0.0004062 1.725352 36.8204112 57 379 proteolysis
124 GO:0036474 0.0004108 7.313867 1.5544237 7 16 cell death in response to hydrogen peroxide
125 GO:0072321 0.0004108 7.313867 1.5544237 7 16 chaperone-mediated protein transport
126 GO:1901031 0.0004108 7.313867 1.5544237 7 16 regulation of response to reactive oxygen species
127 GO:1903902 0.0004108 7.313867 1.5544237 7 16 positive regulation of viral life cycle
128 GO:0051702 0.0004108 7.313867 1.5544237 7 16 interaction with symbiont
129 GO:0051851 0.0004108 7.313867 1.5544237 7 16 modification by host of symbiont morphology or physiology
130 GO:1902904 0.0004625 4.493164 3.0116959 10 31 negative regulation of supramolecular fiber organization
131 GO:0099003 0.0004625 4.493164 3.0116959 10 31 vesicle-mediated transport in synapse
132 GO:0070301 0.0004871 5.793355 2.0401811 8 21 cellular response to hydrogen peroxide
133 GO:1902883 0.0004871 5.793355 2.0401811 8 21 negative regulation of response to oxidative stress
134 GO:0007606 0.0004871 5.793355 2.0401811 8 21 sensory perception of chemical stimulus
135 GO:0008088 0.0004871 5.793355 2.0401811 8 21 axo-dendritic transport
136 GO:0030100 0.0005340 3.995726 3.5946048 11 37 regulation of endocytosis
137 GO:0099504 0.0006153 4.288029 3.1088474 10 32 synaptic vesicle cycle
138 GO:0051085 0.0006405 6.581102 1.6515752 7 17 chaperone cofactor-dependent protein refolding
139 GO:1900407 0.0007013 5.378417 2.1373326 8 22 regulation of cellular response to oxidative stress
140 GO:0006814 0.0007175 3.544235 4.2746652 12 44 sodium ion transport
141 GO:0060236 0.0007677 11.720588 0.8743633 5 9 regulation of mitotic spindle organization
142 GO:0090063 0.0007677 11.720588 0.8743633 5 9 positive regulation of microtubule nucleation
143 GO:0070868 0.0007677 11.720588 0.8743633 5 9 heterochromatin organization involved in chromatin silencing
144 GO:0046685 0.0007677 11.720588 0.8743633 5 9 response to arsenic-containing substance
145 GO:0090224 0.0007677 11.720588 0.8743633 5 9 regulation of spindle organization
146 GO:0097549 0.0007677 11.720588 0.8743633 5 9 chromatin organization involved in negative regulation of transcription
147 GO:0010968 0.0007677 11.720588 0.8743633 5 9 regulation of microtubule nucleation
148 GO:0034401 0.0007677 11.720588 0.8743633 5 9 chromatin organization involved in regulation of transcription
149 GO:1901564 0.0008470 1.358999 169.3350311 202 1743 organonitrogen compound metabolic process
150 GO:0030900 0.0008748 3.708759 3.7889078 11 39 forebrain development
151 GO:0061588 0.0009121 Inf 0.2914544 3 3 calcium activated phospholipid scrambling
152 GO:0007040 0.0009613 5.981568 1.7487267 7 18 lysosome organization
153 GO:0080171 0.0009613 5.981568 1.7487267 7 18 lytic vacuole organization
154 GO:0051084 0.0009613 5.981568 1.7487267 7 18 ‘de novo’ posttranslational protein folding
155 GO:0036473 0.0009851 5.018803 2.2344841 8 23 cell death in response to oxidative stress
156 GO:0043484 0.0009851 5.018803 2.2344841 8 23 regulation of RNA splicing
157 GO:0045862 0.0010464 3.929043 3.3031503 10 34 positive regulation of proteolysis
158 GO:0048260 0.0011263 18.724070 0.5829089 4 6 positive regulation of receptor-mediated endocytosis
159 GO:0018022 0.0012170 4.238537 2.8173929 9 29 peptidyl-lysine methylation
160 GO:0010970 0.0013402 3.771089 3.4003018 10 35 transport along microtubule
161 GO:1903311 0.0013402 3.771089 3.4003018 10 35 regulation of mRNA metabolic process
162 GO:0099111 0.0013402 3.771089 3.4003018 10 35 microtubule-based transport
163 GO:0034614 0.0013540 4.704142 2.3316355 8 24 cellular response to reactive oxygen species
164 GO:0046777 0.0013963 5.481955 1.8458781 7 19 protein autophosphorylation
165 GO:0046686 0.0013963 5.481955 1.8458781 7 19 response to cadmium ion
166 GO:0014823 0.0013963 5.481955 1.8458781 7 19 response to activity
167 GO:0045069 0.0013963 5.481955 1.8458781 7 19 regulation of viral genome replication
168 GO:0002699 0.0013963 5.481955 1.8458781 7 19 positive regulation of immune effector process
169 GO:0045471 0.0013963 5.481955 1.8458781 7 19 response to ethanol
170 GO:0007413 0.0014134 9.374510 0.9715148 5 10 axonal fasciculation
171 GO:0070828 0.0014134 9.374510 0.9715148 5 10 heterochromatin organization
172 GO:0106030 0.0014134 9.374510 0.9715148 5 10 neuron projection fasciculation
173 GO:0032781 0.0014134 9.374510 0.9715148 5 10 positive regulation of ATPase activity
174 GO:0030705 0.0016977 3.625286 3.4974533 10 36 cytoskeleton-dependent intracellular transport
175 GO:0007018 0.0018092 2.679057 6.6063007 15 68 microtubule-based movement
176 GO:1902882 0.0018248 4.426500 2.4287870 8 25 regulation of response to oxidative stress
177 GO:0097237 0.0018248 4.426500 2.4287870 8 25 cellular response to toxic substance
178 GO:0043462 0.0019012 6.256712 1.4572722 6 15 regulation of ATPase activity
179 GO:2001023 0.0019708 5.059207 1.9430296 7 20 regulation of response to drug
180 GO:0048524 0.0019708 5.059207 1.9430296 7 20 positive regulation of viral process
181 GO:0019079 0.0019708 5.059207 1.9430296 7 20 viral genome replication
182 GO:0000302 0.0020537 3.851599 3.0116959 9 31 response to reactive oxygen species
183 GO:0043624 0.0021287 3.490282 3.5946048 10 37 cellular protein complex disassembly
184 GO:0006897 0.0021616 2.525584 7.3835125 16 76 endocytosis
185 GO:0006812 0.0022718 1.819278 20.6932654 34 213 cation transport
186 GO:0032880 0.0023978 2.282386 9.5208451 19 98 regulation of protein localization
187 GO:0048511 0.0024056 2.980852 4.8575740 12 50 rhythmic process
188 GO:0071236 0.0024158 4.179706 2.5259385 8 26 cellular response to antibiotic
189 GO:0031099 0.0024158 4.179706 2.5259385 8 26 regeneration
190 GO:1903842 0.0024267 12.480104 0.6800604 4 7 response to arsenite ion
191 GO:0051170 0.0026165 3.683365 3.1088474 9 32 import into nucleus
192 GO:0016032 0.0026436 3.364922 3.6917563 10 38 viral process
193 GO:0071248 0.0027127 4.696850 2.0401811 7 21 cellular response to metal ion
194 GO:0046785 0.0027127 4.696850 2.0401811 7 21 microtubule polymerization
195 GO:0008037 0.0027127 4.696850 2.0401811 7 21 cell recognition
196 GO:1903747 0.0027127 4.696850 2.0401811 7 21 regulation of establishment of protein localization to mitochondrion
197 GO:0007417 0.0027888 2.063967 12.5325410 23 129 central nervous system development
198 GO:0051225 0.0027955 5.629862 1.5544237 6 16 spindle assembly
199 GO:0002252 0.0034172 2.830616 5.0518770 12 52 immune effector process
200 GO:0051172 0.0035614 1.744683 22.0533862 35 227 negative regulation of nitrogen compound metabolic process
201 GO:0000082 0.0036513 4.382808 2.1373326 7 22 G1/S transition of mitotic cell cycle
202 GO:0071241 0.0036513 4.382808 2.1373326 7 22 cellular response to inorganic substance
203 GO:1903900 0.0036513 4.382808 2.1373326 7 22 regulation of viral life cycle
204 GO:0050776 0.0037308 2.543989 6.4119977 14 66 regulation of immune response
205 GO:0090307 0.0037665 6.693277 1.1658178 5 12 mitotic spindle assembly
206 GO:0009583 0.0037665 6.693277 1.1658178 5 12 detection of light stimulus
207 GO:1900034 0.0037665 6.693277 1.1658178 5 12 regulation of cellular response to heat
208 GO:0042246 0.0039710 5.116985 1.6515752 6 17 tissue regeneration
209 GO:0031110 0.0039710 5.116985 1.6515752 6 17 regulation of microtubule polymerization or depolymerization
210 GO:2001234 0.0040387 3.760158 2.7202415 8 28 negative regulation of apoptotic signaling pathway
211 GO:0019058 0.0040387 3.760158 2.7202415 8 28 viral life cycle
212 GO:0006606 0.0040387 3.760158 2.7202415 8 28 protein import into nucleus
213 GO:0035690 0.0041044 3.387273 3.3031503 9 34 cellular response to drug
214 GO:0043066 0.0042495 2.328842 7.8692699 16 81 negative regulation of apoptotic process
215 GO:0060322 0.0042946 2.144249 10.0066025 19 103 head development
216 GO:0009628 0.0044260 1.840232 16.8072062 28 173 response to abiotic stimulus
217 GO:0009584 0.0044826 9.358121 0.7772118 4 8 detection of visible light
218 GO:0046677 0.0048066 3.037368 3.9832107 10 41 response to antibiotic
219 GO:0007041 0.0048178 4.108022 2.2344841 7 23 lysosomal transport
220 GO:0031109 0.0048178 4.108022 2.2344841 7 23 microtubule polymerization or depolymerization
221 GO:0002697 0.0048178 4.108022 2.2344841 7 23 regulation of immune effector process
222 GO:0006909 0.0050612 3.256309 3.4003018 9 35 phagocytosis
223 GO:1901654 0.0051137 3.580351 2.8173929 8 29 response to ketone
224 GO:0098657 0.0054517 2.258367 8.0635729 16 83 import into cell
225 GO:0006811 0.0055479 1.559118 33.4201094 48 344 ion transport
226 GO:0007020 0.0056379 5.855392 1.2629693 5 13 microtubule nucleation
227 GO:0031112 0.0056379 5.855392 1.2629693 5 13 positive regulation of microtubule polymerization or depolymerization
228 GO:0031116 0.0056379 5.855392 1.2629693 5 13 positive regulation of microtubule polymerization
229 GO:0030162 0.0056805 2.403702 6.7034522 14 69 regulation of proteolysis
230 GO:0001822 0.0061824 3.135046 3.4974533 9 36 kidney development
231 GO:0034599 0.0061824 3.135046 3.4974533 9 36 cellular response to oxidative stress
232 GO:0044843 0.0062441 3.865563 2.3316355 7 24 cell cycle G1/S phase transition
233 GO:0060627 0.0064614 2.571119 5.4404829 12 56 regulation of vesicle-mediated transport
234 GO:0032502 0.0064862 1.377911 71.5034899 91 736 developmental process
235 GO:0031324 0.0066964 1.663298 22.9277495 35 236 negative regulation of cellular metabolic process
236 GO:0051049 0.0066966 1.817936 15.7385399 26 162 regulation of transport
237 GO:0055085 0.0068746 1.469961 44.1067723 60 454 transmembrane transport
238 GO:0043069 0.0069164 2.191978 8.2578759 16 85 negative regulation of programmed cell death
239 GO:0007420 0.0069894 2.077637 9.7151481 18 100 brain development
240 GO:1902850 0.0073586 4.327943 1.8458781 6 19 microtubule cytoskeleton organization involved in mitosis
241 GO:1903214 0.0073586 4.327943 1.8458781 6 19 regulation of protein targeting to mitochondrion
242 GO:1903749 0.0073586 4.327943 1.8458781 6 19 positive regulation of establishment of protein localization to mitochondrion
243 GO:1903955 0.0073586 4.327943 1.8458781 6 19 positive regulation of protein targeting to mitochondrion
244 GO:0048568 0.0073838 2.318381 6.8977551 14 71 embryonic organ development
245 GO:0031400 0.0073838 2.318381 6.8977551 14 71 negative regulation of protein modification process
246 GO:0060760 0.0074545 7.484932 0.8743633 4 9 positive regulation of response to cytokine stimulus
247 GO:0060759 0.0074545 7.484932 0.8743633 4 9 regulation of response to cytokine stimulus
248 GO:0048259 0.0074545 7.484932 0.8743633 4 9 regulation of receptor-mediated endocytosis
249 GO:0007339 0.0074545 7.484932 0.8743633 4 9 binding of sperm to zona pellucida
250 GO:0001961 0.0074545 7.484932 0.8743633 4 9 positive regulation of cytokine-mediated signaling pathway
251 GO:0001959 0.0074545 7.484932 0.8743633 4 9 regulation of cytokine-mediated signaling pathway
252 GO:0035036 0.0074545 7.484932 0.8743633 4 9 sperm-egg recognition
253 GO:0009988 0.0074545 7.484932 0.8743633 4 9 cell-cell recognition
254 GO:0048513 0.0076372 1.501865 37.4033201 52 385 animal organ development
255 GO:0007275 0.0076828 1.397620 60.2339181 78 620 multicellular organism development
256 GO:0032677 0.0078502 14.015625 0.4857574 3 5 regulation of interleukin-8 production
257 GO:0032637 0.0078502 14.015625 0.4857574 3 5 interleukin-8 production
258 GO:1902380 0.0078502 14.015625 0.4857574 3 5 positive regulation of endoribonuclease activity
259 GO:0060700 0.0078502 14.015625 0.4857574 3 5 regulation of ribonuclease activity
260 GO:0070370 0.0078502 14.015625 0.4857574 3 5 cellular heat acclimation
261 GO:0060699 0.0078502 14.015625 0.4857574 3 5 regulation of endoribonuclease activity
262 GO:0097035 0.0078502 14.015625 0.4857574 3 5 regulation of membrane lipid distribution
263 GO:0017121 0.0078502 14.015625 0.4857574 3 5 phospholipid scrambling
264 GO:0097201 0.0078502 14.015625 0.4857574 3 5 negative regulation of transcription from RNA polymerase II promoter in response to stress
265 GO:0032757 0.0078502 14.015625 0.4857574 3 5 positive regulation of interleukin-8 production
266 GO:0007519 0.0079042 3.267644 3.0116959 8 31 skeletal muscle tissue development
267 GO:0050792 0.0079627 3.650044 2.4287870 7 25 regulation of viral process
268 GO:0051783 0.0079627 3.650044 2.4287870 7 25 regulation of nuclear division
269 GO:0007052 0.0080804 5.203704 1.3601207 5 14 mitotic spindle organization
270 GO:0001700 0.0080804 5.203704 1.3601207 5 14 embryonic development via the syncytial blastoderm
271 GO:0031113 0.0080804 5.203704 1.3601207 5 14 regulation of microtubule polymerization
272 GO:0016246 0.0080804 5.203704 1.3601207 5 14 RNA interference
273 GO:0048731 0.0082078 1.427018 50.6159215 67 521 system development
274 GO:0048856 0.0085855 1.377038 64.9943407 83 669 anatomical structure development
275 GO:0032269 0.0086032 2.027307 9.9094510 18 102 negative regulation of cellular protein metabolic process
276 GO:0032501 0.0087486 1.358400 72.2807018 91 744 multicellular organismal process
277 GO:0045934 0.0093500 1.833385 13.7955103 23 142 negative regulation of nucleobase-containing compound metabolic process
278 GO:0042493 0.0095156 2.003030 10.0066025 18 103 response to drug
279 GO:0044403 0.0096109 2.687977 4.3718166 10 45 symbiont process
280 GO:0009566 0.0096677 4.017962 1.9430296 6 20 fertilization
281 GO:1903533 0.0096677 4.017962 1.9430296 6 20 regulation of protein targeting
282 GO:0032886 0.0100063 3.457211 2.5259385 7 26 regulation of microtubule-based process
283 GO:0044743 0.0100063 3.457211 2.5259385 7 26 protein transmembrane import into intracellular organelle
284 GO:0007338 0.0111699 4.682353 1.4572722 5 15 single fertilization
285 GO:0001895 0.0111699 4.682353 1.4572722 5 15 retina homeostasis
286 GO:0010921 0.0111699 4.682353 1.4572722 5 15 regulation of phosphatase activity
287 GO:0019221 0.0111699 4.682353 1.4572722 5 15 cytokine-mediated signaling pathway
288 GO:0009605 0.0111809 1.620567 22.0533862 33 227 response to external stimulus
289 GO:0008213 0.0112465 2.612761 4.4689681 10 46 protein alkylation
290 GO:0006479 0.0112465 2.612761 4.4689681 10 46 protein methylation
291 GO:0009636 0.0114187 2.465231 5.1490285 11 53 response to toxic substance
292 GO:2001237 0.0114818 6.236138 0.9715148 4 10 negative regulation of extrinsic apoptotic signaling pathway
293 GO:0046688 0.0114818 6.236138 0.9715148 4 10 response to copper ion
294 GO:0021695 0.0114818 6.236138 0.9715148 4 10 cerebellar cortex development
295 GO:0021680 0.0114818 6.236138 0.9715148 4 10 cerebellar Purkinje cell layer development
296 GO:0043666 0.0114818 6.236138 0.9715148 4 10 regulation of phosphoprotein phosphatase activity
297 GO:1902115 0.0117057 3.004970 3.2059989 8 33 regulation of organelle assembly
298 GO:0060538 0.0117057 3.004970 3.2059989 8 33 skeletal muscle organ development
299 GO:0051129 0.0119870 2.041705 8.7436333 16 90 negative regulation of cellular component organization
300 GO:0007088 0.0124497 3.749312 2.0401811 6 21 regulation of mitotic nuclear division
301 GO:0050790 0.0124927 1.660717 18.9445388 29 195 regulation of catalytic activity
302 GO:0072001 0.0126644 2.728229 3.8860592 9 40 renal system development
303 GO:0031647 0.0126644 2.728229 3.8860592 9 40 regulation of protein stability
304 GO:0002682 0.0127252 1.933510 10.2980570 18 106 regulation of immune system process
305 GO:0044267 0.0130139 1.276784 115.2216563 136 1186 cellular protein metabolic process
306 GO:0044419 0.0130846 2.541611 4.5661196 10 47 interspecies interaction between organisms
307 GO:0080135 0.0132848 2.014055 8.8407848 16 91 regulation of cellular response to stress
308 GO:0032268 0.0136985 1.559841 24.8707791 36 256 regulation of cellular protein metabolic process
309 GO:0022414 0.0138877 1.629808 19.9160536 30 205 reproductive process
310 GO:0007600 0.0140919 2.187322 6.7034522 13 69 sensory perception
311 GO:0010803 0.0145740 9.341797 0.5829089 3 6 regulation of tumor necrosis factor-mediated signaling pathway
312 GO:1903265 0.0145740 9.341797 0.5829089 3 6 positive regulation of tumor necrosis factor-mediated signaling pathway
313 GO:0032069 0.0145740 9.341797 0.5829089 3 6 regulation of nuclease activity
314 GO:0032075 0.0145740 9.341797 0.5829089 3 6 positive regulation of nuclease activity
315 GO:0002931 0.0145740 9.341797 0.5829089 3 6 response to ischemia
316 GO:0036010 0.0145740 9.341797 0.5829089 3 6 protein localization to endosome
317 GO:0097305 0.0148744 2.642416 3.9832107 9 41 response to alcohol
318 GO:0001890 0.0149765 4.255793 1.5544237 5 16 placenta development
319 GO:2001236 0.0149765 4.255793 1.5544237 5 16 regulation of extrinsic apoptotic signaling pathway
320 GO:0008038 0.0149765 4.255793 1.5544237 5 16 neuron recognition
321 GO:0002376 0.0150403 1.664147 17.5844180 27 181 immune system process
322 GO:0031327 0.0151111 1.743138 14.3784192 23 148 negative regulation of cellular biosynthetic process
323 GO:0032271 0.0151395 2.474205 4.6632711 10 48 regulation of protein polymerization
324 GO:0051248 0.0153019 1.889738 10.4923599 18 108 negative regulation of protein metabolic process
325 GO:0042981 0.0154551 1.818959 12.0467836 20 124 regulation of apoptotic process
326 GO:0007051 0.0157491 3.514244 2.1373326 6 22 spindle organization
327 GO:0090316 0.0157491 3.514244 2.1373326 6 22 positive regulation of intracellular protein transport
328 GO:1902903 0.0165463 2.214946 6.1205433 12 63 regulation of supramolecular fiber organization
329 GO:1903169 0.0166796 5.344143 1.0686663 4 11 regulation of calcium ion transmembrane transport
330 GO:0045646 0.0166796 5.344143 1.0686663 4 11 regulation of erythrocyte differentiation
331 GO:2001233 0.0173560 2.561804 4.0803622 9 42 regulation of apoptotic signaling pathway
332 GO:0032984 0.0174255 2.410256 4.7604226 10 49 protein-containing complex disassembly
333 GO:0000003 0.0183950 1.575209 21.1790228 31 218 reproduction
334 GO:0071806 0.0184048 2.983894 2.8173929 7 29 protein transmembrane transport
335 GO:0043903 0.0184048 2.983894 2.8173929 7 29 regulation of symbiosis, encompassing mutualism through parasitism
336 GO:0009890 0.0188972 1.701188 14.6698736 23 151 negative regulation of biosynthetic process
337 GO:0009611 0.0194123 2.248965 5.5376344 11 57 response to wounding
338 GO:1903827 0.0194123 2.248965 5.5376344 11 57 regulation of cellular protein localization
339 GO:0051345 0.0194123 2.248965 5.5376344 11 57 positive regulation of hydrolase activity
340 GO:0070507 0.0196072 3.306830 2.2344841 6 23 regulation of microtubule cytoskeleton organization
341 GO:0010822 0.0196072 3.306830 2.2344841 6 23 positive regulation of mitochondrion organization
342 GO:0044087 0.0197342 1.766827 12.3382381 20 127 regulation of cellular component biogenesis
343 GO:0097435 0.0198721 1.795040 11.5610262 19 119 supramolecular fiber organization
344 GO:0050877 0.0199115 1.827611 10.7838144 18 111 nervous system process
345 GO:0001816 0.0201266 2.485933 4.1775137 9 43 cytokine production
346 GO:0001655 0.0201266 2.485933 4.1775137 9 43 urogenital system development
347 GO:0035966 0.0201266 2.485933 4.1775137 9 43 response to topologically incorrect protein
348 GO:0010558 0.0207124 1.705982 13.9898132 22 144 negative regulation of macromolecule biosynthetic process
349 GO:0043067 0.0213482 1.750093 12.4353895 20 128 regulation of programmed cell death
350 GO:0060548 0.0214952 1.886172 9.3265422 16 96 negative regulation of cell death
351 GO:0050778 0.0227463 2.291717 4.9547255 10 51 positive regulation of immune response
352 GO:0045892 0.0230621 1.733667 12.5325410 20 129 negative regulation of transcription, DNA-templated
353 GO:0031101 0.0231361 4.675147 1.1658178 4 12 fin regeneration
354 GO:0042098 0.0231361 4.675147 1.1658178 4 12 T cell proliferation
355 GO:0048585 0.0233896 1.661159 14.9613281 23 154 negative regulation of response to stimulus
356 GO:0043086 0.0233943 2.090568 6.4119977 12 66 negative regulation of catalytic activity
357 GO:0007351 0.0236845 7.004883 0.6800604 3 7 tripartite regional subdivision
358 GO:1902236 0.0236845 7.004883 0.6800604 3 7 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
359 GO:0010286 0.0236845 7.004883 0.6800604 3 7 heat acclimation
360 GO:1901019 0.0236845 7.004883 0.6800604 3 7 regulation of calcium ion transmembrane transporter activity
361 GO:0002753 0.0236845 7.004883 0.6800604 3 7 cytoplasmic pattern recognition receptor signaling pathway
362 GO:0008595 0.0236845 7.004883 0.6800604 3 7 anterior/posterior axis specification, embryo
363 GO:0045648 0.0236845 7.004883 0.6800604 3 7 positive regulation of erythrocyte differentiation
364 GO:0045639 0.0236845 7.004883 0.6800604 3 7 positive regulation of myeloid cell differentiation
365 GO:0051246 0.0239665 1.479167 26.7166572 37 275 regulation of protein metabolic process
366 GO:1903828 0.0249799 3.599547 1.7487267 5 18 negative regulation of cellular protein localization
367 GO:0006955 0.0256871 1.839386 9.5208451 16 98 immune response
368 GO:0001894 0.0261889 2.734088 3.0116959 7 31 tissue homeostasis
369 GO:0060433 0.0264413 18.654971 0.2914544 2 3 bronchus development
370 GO:0032958 0.0264413 18.654971 0.2914544 2 3 inositol phosphate biosynthetic process
371 GO:0036270 0.0264413 18.654971 0.2914544 2 3 response to diuretic
372 GO:0042533 0.0264413 18.654971 0.2914544 2 3 tumor necrosis factor biosynthetic process
373 GO:0042534 0.0264413 18.654971 0.2914544 2 3 regulation of tumor necrosis factor biosynthetic process
374 GO:0007354 0.0264413 18.654971 0.2914544 2 3 zygotic determination of anterior/posterior axis, embryo
375 GO:0070424 0.0264413 18.654971 0.2914544 2 3 regulation of nucleotide-binding oligomerization domain containing signaling pathway
376 GO:0070426 0.0264413 18.654971 0.2914544 2 3 positive regulation of nucleotide-binding oligomerization domain containing signaling pathway
377 GO:0070431 0.0264413 18.654971 0.2914544 2 3 nucleotide-binding oligomerization domain containing 2 signaling pathway
378 GO:0070432 0.0264413 18.654971 0.2914544 2 3 regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway
379 GO:0070434 0.0264413 18.654971 0.2914544 2 3 positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway
380 GO:0070194 0.0264413 18.654971 0.2914544 2 3 synaptonemal complex disassembly
381 GO:0007218 0.0264413 18.654971 0.2914544 2 3 neuropeptide signaling pathway
382 GO:0031000 0.0264413 18.654971 0.2914544 2 3 response to caffeine
383 GO:2001240 0.0264413 18.654971 0.2914544 2 3 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
384 GO:2001239 0.0264413 18.654971 0.2914544 2 3 regulation of extrinsic apoptotic signaling pathway in absence of ligand
385 GO:0097192 0.0264413 18.654971 0.2914544 2 3 extrinsic apoptotic signaling pathway in absence of ligand
386 GO:1902946 0.0264413 18.654971 0.2914544 2 3 protein localization to early endosome
387 GO:1901099 0.0264413 18.654971 0.2914544 2 3 negative regulation of signal transduction in absence of ligand
388 GO:0045109 0.0264413 18.654971 0.2914544 2 3 intermediate filament organization
389 GO:1901894 0.0264413 18.654971 0.2914544 2 3 regulation of calcium-transporting ATPase activity
390 GO:1901896 0.0264413 18.654971 0.2914544 2 3 positive regulation of calcium-transporting ATPase activity
391 GO:0038034 0.0264413 18.654971 0.2914544 2 3 signal transduction in absence of ligand
392 GO:0018992 0.0264413 18.654971 0.2914544 2 3 germ-line sex determination
393 GO:1902679 0.0268047 1.701702 12.7268440 20 131 negative regulation of RNA biosynthetic process
394 GO:1903507 0.0268047 1.701702 12.7268440 20 131 negative regulation of nucleic acid-templated transcription
395 GO:0070585 0.0268459 2.501512 3.6917563 8 38 protein localization to mitochondrion
396 GO:0072655 0.0268459 2.501512 3.6917563 8 38 establishment of protein localization to mitochondrion
397 GO:0007399 0.0269273 1.442424 29.5340502 40 304 nervous system development
398 GO:0044092 0.0276224 1.910324 8.0635729 14 83 negative regulation of molecular function
399 GO:0051179 0.0276749 1.230281 123.6738351 142 1273 localization
400 GO:0051258 0.0276906 2.109937 5.8290889 11 60 protein polymerization
401 GO:0051336 0.0278907 1.781169 10.3952085 17 107 regulation of hydrolase activity
402 GO:2000113 0.0282115 1.667183 13.6012073 21 140 negative regulation of cellular macromolecule biosynthetic process
403 GO:0051253 0.0288406 1.686147 12.8239955 20 132 negative regulation of RNA metabolic process
404 GO:0051050 0.0305040 1.834675 8.9379362 15 92 positive regulation of transport
405 GO:0048869 0.0307788 1.361204 41.2893794 53 425 cellular developmental process
406 GO:0043902 0.0308151 2.624173 3.1088474 7 32 positive regulation of multi-organism process
407 GO:0042119 0.0309130 4.154816 1.2629693 4 13 neutrophil activation
408 GO:0036230 0.0309130 4.154816 1.2629693 4 13 granulocyte activation
409 GO:0007350 0.0309130 4.154816 1.2629693 4 13 blastoderm segmentation
410 GO:0009190 0.0309130 4.154816 1.2629693 4 13 cyclic nucleotide biosynthetic process
411 GO:0002444 0.0309130 4.154816 1.2629693 4 13 myeloid leukocyte mediated immunity
412 GO:0002446 0.0309130 4.154816 1.2629693 4 13 neutrophil mediated immunity
413 GO:0009187 0.0309130 4.154816 1.2629693 4 13 cyclic nucleotide metabolic process
414 GO:0042594 0.0310104 2.420309 3.7889078 8 39 response to starvation
415 GO:0009416 0.0310104 2.420309 3.7889078 8 39 response to light stimulus
416 GO:0032273 0.0310104 2.420309 3.7889078 8 39 positive regulation of protein polymerization
417 GO:0051924 0.0312733 3.341737 1.8458781 5 19 regulation of calcium ion transport
418 GO:2001243 0.0312733 3.341737 1.8458781 5 19 negative regulation of intrinsic apoptotic signaling pathway
419 GO:0097191 0.0312733 3.341737 1.8458781 5 19 extrinsic apoptotic signaling pathway
420 GO:0030218 0.0312733 3.341737 1.8458781 5 19 erythrocyte differentiation
421 GO:0002262 0.0312733 3.341737 1.8458781 5 19 myeloid cell homeostasis
422 GO:0035303 0.0312733 3.341737 1.8458781 5 19 regulation of dephosphorylation
423 GO:0034101 0.0312733 3.341737 1.8458781 5 19 erythrocyte homeostasis
424 GO:0048523 0.0321128 1.342633 44.9811356 57 463 negative regulation of cellular process
425 GO:0061061 0.0330845 1.773335 9.8122996 16 101 muscle structure development
426 GO:0030154 0.0337976 1.359492 39.7349557 51 409 cell differentiation
427 GO:0042060 0.0344215 2.222384 4.5661196 9 47 wound healing
428 GO:0009581 0.0348872 2.809037 2.5259385 6 26 detection of external stimulus
429 GO:0009582 0.0348872 2.809037 2.5259385 6 26 detection of abiotic stimulus
430 GO:0060711 0.0352056 5.602734 0.7772118 3 8 labyrinthine layer development
431 GO:1902235 0.0352056 5.602734 0.7772118 3 8 regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
432 GO:0033209 0.0352056 5.602734 0.7772118 3 8 tumor necrosis factor-mediated signaling pathway
433 GO:0007602 0.0352056 5.602734 0.7772118 3 8 phototransduction
434 GO:0006298 0.0352056 5.602734 0.7772118 3 8 mismatch repair
435 GO:0001817 0.0355969 2.344181 3.8860592 8 40 regulation of cytokine production
436 GO:0030001 0.0356499 1.641107 13.1154499 20 135 metal ion transport
437 GO:0007033 0.0359599 2.522714 3.2059989 7 33 vacuole organization
438 GO:0060341 0.0361791 1.787468 9.1322392 15 94 regulation of cellular localization
439 GO:1901701 0.0362689 1.829563 8.3550274 14 86 cellular response to oxygen-containing compound
440 GO:0006810 0.0365383 1.226460 106.6723260 123 1098 transport
441 GO:0051234 0.0380542 1.221677 109.6840219 126 1129 establishment of localization
442 GO:0051247 0.0381651 1.626611 13.2126014 20 136 positive regulation of protein metabolic process
443 GO:0002684 0.0382497 1.986951 6.1205433 11 63 positive regulation of immune system process
444 GO:0010605 0.0388499 1.423591 26.8138087 36 276 negative regulation of macromolecule metabolic process
445 GO:0032943 0.0400461 3.738552 1.3601207 4 14 mononuclear cell proliferation
446 GO:0070661 0.0400461 3.738552 1.3601207 4 14 leukocyte proliferation
447 GO:0046651 0.0400461 3.738552 1.3601207 4 14 lymphocyte proliferation
448 GO:1903321 0.0400461 3.738552 1.3601207 4 14 negative regulation of protein modification by small protein conjugation or removal
449 GO:0035304 0.0400461 3.738552 1.3601207 4 14 regulation of protein dephosphorylation
450 GO:0014706 0.0410174 2.040465 5.4404829 10 56 striated muscle tissue development
451 GO:0022008 0.0412701 1.475729 20.8875684 29 215 neurogenesis
452 GO:0010821 0.0413101 2.674712 2.6230900 6 27 regulation of mitochondrion organization
453 GO:0032388 0.0413101 2.674712 2.6230900 6 27 positive regulation of intracellular transport
454 GO:0031399 0.0428127 1.531788 16.7100547 24 172 regulation of protein modification process
455 GO:0033365 0.0431715 1.646657 11.7553292 18 121 protein localization to organelle
456 GO:0048519 0.0443329 1.289811 53.1418600 65 547 negative regulation of biological process
457 GO:0032270 0.0449481 1.613357 12.6296925 19 130 positive regulation of cellular protein metabolic process
458 GO:0043254 0.0456143 1.996630 5.5376344 10 57 regulation of protein complex assembly
459 GO:0048584 0.0461335 1.504290 17.6815695 25 182 positive regulation of response to stimulus
460 GO:0065009 0.0466520 1.413101 25.4536880 34 262 regulation of molecular function
461 GO:0051169 0.0466814 1.912551 6.3148463 11 65 nuclear transport
462 GO:0048871 0.0478755 2.341535 3.4003018 7 35 multicellular organismal homeostasis
463 GO:1903829 0.0478755 2.341535 3.4003018 7 35 positive regulation of cellular protein localization
464 GO:0009792 0.0487092 1.673035 10.2980570 16 106 embryo development ending in birth or egg hatching
465 GO:0010038 0.0489077 2.058469 4.8575740 9 50 response to metal ion
466 GO:0071356 0.0490812 4.667969 0.8743633 3 9 cellular response to tumor necrosis factor
467 GO:0070059 0.0490812 4.667969 0.8743633 3 9 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
468 GO:0031397 0.0490812 4.667969 0.8743633 3 9 negative regulation of protein ubiquitination
469 GO:1903708 0.0490812 4.667969 0.8743633 3 9 positive regulation of hemopoiesis
470 GO:1904376 0.0494985 9.325536 0.3886059 2 4 negative regulation of protein localization to cell periphery
471 GO:1902044 0.0494985 9.325536 0.3886059 2 4 regulation of Fas signaling pathway
472 GO:1902045 0.0494985 9.325536 0.3886059 2 4 negative regulation of Fas signaling pathway
473 GO:0036337 0.0494985 9.325536 0.3886059 2 4 Fas signaling pathway
474 GO:0060710 0.0494985 9.325536 0.3886059 2 4 chorio-allantoic fusion
475 GO:0060715 0.0494985 9.325536 0.3886059 2 4 syncytiotrophoblast cell differentiation involved in labyrinthine layer development
476 GO:0050962 0.0494985 9.325536 0.3886059 2 4 detection of light stimulus involved in sensory perception
477 GO:0050921 0.0494985 9.325536 0.3886059 2 4 positive regulation of chemotaxis
478 GO:0050908 0.0494985 9.325536 0.3886059 2 4 detection of light stimulus involved in visual perception
479 GO:0070423 0.0494985 9.325536 0.3886059 2 4 nucleotide-binding oligomerization domain containing signaling pathway
480 GO:0007422 0.0494985 9.325536 0.3886059 2 4 peripheral nervous system development
481 GO:0007530 0.0494985 9.325536 0.3886059 2 4 sex determination
482 GO:0007603 0.0494985 9.325536 0.3886059 2 4 phototransduction, visible light
483 GO:0043101 0.0494985 9.325536 0.3886059 2 4 purine-containing compound salvage
484 GO:1903077 0.0494985 9.325536 0.3886059 2 4 negative regulation of protein localization to plasma membrane
485 GO:0015697 0.0494985 9.325536 0.3886059 2 4 quaternary ammonium group transport
486 GO:2000514 0.0494985 9.325536 0.3886059 2 4 regulation of CD4-positive, alpha-beta T cell activation
487 GO:2000504 0.0494985 9.325536 0.3886059 2 4 positive regulation of blood vessel remodeling
488 GO:0072132 0.0494985 9.325536 0.3886059 2 4 mesenchyme morphogenesis
489 GO:0006013 0.0494985 9.325536 0.3886059 2 4 mannose metabolic process
490 GO:0016056 0.0494985 9.325536 0.3886059 2 4 rhodopsin mediated signaling pathway
491 GO:0035710 0.0494985 9.325536 0.3886059 2 4 CD4-positive, alpha-beta T cell activation
492 GO:0035872 0.0494985 9.325536 0.3886059 2 4 nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
493 GO:0032469 0.0494985 9.325536 0.3886059 2 4 endoplasmic reticulum calcium ion homeostasis
494 GO:1905476 0.0494985 9.325536 0.3886059 2 4 negative regulation of protein localization to membrane
Module 5
GO_term_green <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_green.csv")
GO_term_green %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0055114 0.0000000 3.874922 14.1482739 43 300 oxidation-reduction process
2 GO:0006629 0.0000000 3.294290 13.6766648 37 290 lipid metabolic process
3 GO:0044255 0.0000026 3.177618 9.6208263 26 204 cellular lipid metabolic process
4 GO:0006720 0.0000044 9.393983 1.3676665 9 29 isoprenoid metabolic process
5 GO:0044281 0.0000046 2.357653 21.3167327 43 452 small molecule metabolic process
6 GO:0019752 0.0000070 3.059636 9.5265044 25 202 carboxylic acid metabolic process
7 GO:0043436 0.0000084 3.024209 9.6208263 25 204 oxoacid metabolic process
8 GO:0006082 0.0000084 3.024209 9.6208263 25 204 organic acid metabolic process
9 GO:0006066 0.0000108 8.163810 1.5091492 9 32 alcohol metabolic process
10 GO:0055085 0.0000122 2.273595 21.4110545 42 454 transmembrane transport
11 GO:0034754 0.0000465 20.595918 0.4716091 5 10 cellular hormone metabolic process
12 GO:0032787 0.0000742 4.417514 3.2541030 12 69 monocarboxylic acid metabolic process
13 GO:1901615 0.0000902 4.698318 2.8296548 11 60 organic hydroxy compound metabolic process
14 GO:0106120 0.0001037 Inf 0.1414827 3 3 positive regulation of sterol biosynthetic process
15 GO:0045940 0.0001037 Inf 0.1414827 3 3 positive regulation of steroid metabolic process
16 GO:0010893 0.0001037 Inf 0.1414827 3 3 positive regulation of steroid biosynthetic process
17 GO:1902932 0.0001037 Inf 0.1414827 3 3 positive regulation of alcohol biosynthetic process
18 GO:0090205 0.0001037 Inf 0.1414827 3 3 positive regulation of cholesterol metabolic process
19 GO:0045542 0.0001037 Inf 0.1414827 3 3 positive regulation of cholesterol biosynthetic process
20 GO:0006631 0.0001375 5.510496 2.0279193 9 43 fatty acid metabolic process
21 GO:0008610 0.0001393 3.252466 5.6593096 16 120 lipid biosynthetic process
22 GO:0016042 0.0003325 4.799234 2.2637238 9 48 lipid catabolic process
23 GO:0090181 0.0004003 61.336032 0.1886437 3 4 regulation of cholesterol metabolic process
24 GO:0045540 0.0004003 61.336032 0.1886437 3 4 regulation of cholesterol biosynthetic process
25 GO:0042445 0.0004081 7.738217 1.0375401 6 22 hormone metabolic process
26 GO:0006732 0.0005438 3.703536 3.4427467 11 73 coenzyme metabolic process
27 GO:0001523 0.0008096 13.672087 0.4716091 4 10 retinoid metabolic process
28 GO:0009074 0.0008096 13.672087 0.4716091 4 10 aromatic amino acid family catabolic process
29 GO:0016126 0.0008096 13.672087 0.4716091 4 10 sterol biosynthetic process
30 GO:0016101 0.0008096 13.672087 0.4716091 4 10 diterpenoid metabolic process
31 GO:0045834 0.0008096 13.672087 0.4716091 4 10 positive regulation of lipid metabolic process
32 GO:0009108 0.0008231 4.154357 2.5466893 9 54 coenzyme biosynthetic process
33 GO:0008202 0.0008581 5.360158 1.6034710 7 34 steroid metabolic process
34 GO:0006694 0.0008598 6.512511 1.1790228 6 25 steroid biosynthetic process
35 GO:0106118 0.0009658 30.661943 0.2358046 3 5 regulation of sterol biosynthetic process
36 GO:0050810 0.0009658 30.661943 0.2358046 3 5 regulation of steroid biosynthetic process
37 GO:0046889 0.0009658 30.661943 0.2358046 3 5 positive regulation of lipid biosynthetic process
38 GO:1902930 0.0009658 30.661943 0.2358046 3 5 regulation of alcohol biosynthetic process
39 GO:0019218 0.0009658 30.661943 0.2358046 3 5 regulation of steroid metabolic process
40 GO:0006695 0.0009658 30.661943 0.2358046 3 5 cholesterol biosynthetic process
41 GO:0046395 0.0010302 5.167695 1.6506320 7 35 carboxylic acid catabolic process
42 GO:0016054 0.0010302 5.167695 1.6506320 7 35 organic acid catabolic process
43 GO:1901605 0.0010321 4.479786 2.1222411 8 45 alpha-amino acid metabolic process
44 GO:0006721 0.0012254 11.716609 0.5187700 4 11 terpenoid metabolic process
45 GO:0044242 0.0012283 4.988506 1.6977929 7 36 cellular lipid catabolic process
46 GO:0044282 0.0013877 4.248358 2.2165629 8 47 small molecule catabolic process
47 GO:1901617 0.0019679 5.375624 1.3676665 6 29 organic hydroxy compound biosynthetic process
48 GO:0051186 0.0021753 2.743724 5.2820223 13 112 cofactor metabolic process
49 GO:0097089 0.0022157 Inf 0.0943218 2 2 methyl-branched fatty acid metabolic process
50 GO:0001561 0.0022157 Inf 0.0943218 2 2 fatty acid alpha-oxidation
51 GO:0006103 0.0022157 Inf 0.0943218 2 2 2-oxoglutarate metabolic process
52 GO:0062013 0.0031493 15.324899 0.3301264 3 7 positive regulation of small molecule metabolic process
53 GO:1902653 0.0031493 15.324899 0.3301264 3 7 secondary alcohol biosynthetic process
54 GO:0008203 0.0031493 15.324899 0.3301264 3 7 cholesterol metabolic process
55 GO:0016125 0.0033226 8.196748 0.6602528 4 14 sterol metabolic process
56 GO:0006576 0.0033226 8.196748 0.6602528 4 14 cellular biogenic amine metabolic process
57 GO:0051188 0.0042917 3.159716 3.2069421 9 68 cofactor biosynthetic process
58 GO:0046165 0.0056075 6.827913 0.7545746 4 16 alcohol biosynthetic process
59 GO:0008299 0.0056075 6.827913 0.7545746 4 16 isoprenoid biosynthetic process
60 GO:0036367 0.0064396 40.725806 0.1414827 2 3 light adaption
61 GO:0023058 0.0064396 40.725806 0.1414827 2 3 adaptation of signaling pathway
62 GO:0052803 0.0064396 40.725806 0.1414827 2 3 imidazole-containing compound metabolic process
63 GO:0052805 0.0064396 40.725806 0.1414827 2 3 imidazole-containing compound catabolic process
64 GO:0016062 0.0064396 40.725806 0.1414827 2 3 adaptation of rhodopsin mediated signaling
65 GO:0009644 0.0064396 40.725806 0.1414827 2 3 response to high light intensity
66 GO:0006563 0.0064396 40.725806 0.1414827 2 3 L-serine metabolic process
67 GO:0006547 0.0064396 40.725806 0.1414827 2 3 histidine metabolic process
68 GO:0006548 0.0064396 40.725806 0.1414827 2 3 histidine catabolic process
69 GO:1902652 0.0070443 10.212551 0.4244482 3 9 secondary alcohol metabolic process
70 GO:0034308 0.0070443 10.212551 0.4244482 3 9 primary alcohol metabolic process
71 GO:0044283 0.0070626 2.446367 5.3763441 12 114 small molecule biosynthetic process
72 GO:0009072 0.0070654 6.301438 0.8017355 4 17 aromatic amino acid family metabolic process
73 GO:0006081 0.0087533 5.850174 0.8488964 4 18 cellular aldehyde metabolic process
74 GO:0006665 0.0087533 5.850174 0.8488964 4 18 sphingolipid metabolic process
75 GO:0006520 0.0100716 2.427090 4.9518959 11 105 cellular amino acid metabolic process
76 GO:0097164 0.0105011 4.274660 1.3676665 5 29 ammonium ion metabolic process
77 GO:0009308 0.0106845 5.459079 0.8960573 4 19 amine metabolic process
78 GO:1901607 0.0106845 5.459079 0.8960573 4 19 alpha-amino acid biosynthetic process
79 GO:0044106 0.0106845 5.459079 0.8960573 4 19 cellular amine metabolic process
80 GO:0042572 0.0124790 20.358871 0.1886437 2 4 retinol metabolic process
81 GO:0042574 0.0124790 20.358871 0.1886437 2 4 retinal metabolic process
82 GO:0046473 0.0124790 20.358871 0.1886437 2 4 phosphatidic acid metabolic process
83 GO:0007603 0.0124790 20.358871 0.1886437 2 4 phototransduction, visible light
84 GO:0043545 0.0124790 20.358871 0.1886437 2 4 molybdopterin cofactor metabolic process
85 GO:0019720 0.0124790 20.358871 0.1886437 2 4 Mo-molybdopterin cofactor metabolic process
86 GO:0016056 0.0124790 20.358871 0.1886437 2 4 rhodopsin mediated signaling pathway
87 GO:0032367 0.0124790 20.358871 0.1886437 2 4 intracellular cholesterol transport
88 GO:0051189 0.0124790 20.358871 0.1886437 2 4 prosthetic group metabolic process
89 GO:0006777 0.0124790 20.358871 0.1886437 2 4 Mo-molybdopterin cofactor biosynthetic process
90 GO:0006654 0.0124790 20.358871 0.1886437 2 4 phosphatidic acid biosynthetic process
91 GO:0006685 0.0124790 20.358871 0.1886437 2 4 sphingomyelin catabolic process
92 GO:0008652 0.0128711 5.116870 0.9432183 4 20 cellular amino acid biosynthetic process
93 GO:1901606 0.0128711 5.116870 0.9432183 4 20 alpha-amino acid catabolic process
94 GO:0019395 0.0129005 7.656377 0.5187700 3 11 fatty acid oxidation
95 GO:0034440 0.0129005 7.656377 0.5187700 3 11 lipid oxidation
96 GO:0009062 0.0166104 6.804318 0.5659310 3 12 fatty acid catabolic process
97 GO:0007186 0.0189731 2.107819 6.1309187 12 130 G protein-coupled receptor signaling pathway
98 GO:0046394 0.0200228 2.769310 2.7824939 7 59 carboxylic acid biosynthetic process
99 GO:0016053 0.0200228 2.769310 2.7824939 7 59 organic acid biosynthetic process
100 GO:2001238 0.0201544 13.569892 0.2358046 2 5 positive regulation of extrinsic apoptotic signaling pathway
101 GO:0006684 0.0201544 13.569892 0.2358046 2 5 sphingomyelin metabolic process
102 GO:0072329 0.0208545 6.122672 0.6130919 3 13 monocarboxylic acid catabolic process
103 GO:0043648 0.0208545 6.122672 0.6130919 3 13 dicarboxylic acid metabolic process
104 GO:0009063 0.0210631 4.306376 1.0847010 4 23 cellular amino acid catabolic process
105 GO:1901071 0.0241283 2.932670 2.2637238 6 48 glucosamine-containing compound metabolic process
106 GO:0046890 0.0256359 5.564961 0.6602528 3 14 regulation of lipid biosynthetic process
107 GO:0010817 0.0264481 2.863896 2.3108847 6 49 regulation of hormone levels
108 GO:0006040 0.0264481 2.863896 2.3108847 6 49 amino sugar metabolic process
109 GO:0042401 0.0292995 10.175403 0.2829655 2 6 cellular biogenic amine biosynthetic process
110 GO:0042559 0.0292995 10.175403 0.2829655 2 6 pteridine-containing compound biosynthetic process
111 GO:0009070 0.0292995 10.175403 0.2829655 2 6 serine family amino acid biosynthetic process
112 GO:0009309 0.0292995 10.175403 0.2829655 2 6 amine biosynthetic process
113 GO:0009435 0.0292995 10.175403 0.2829655 2 6 NAD biosynthetic process
114 GO:0009642 0.0292995 10.175403 0.2829655 2 6 response to light intensity
115 GO:0032366 0.0292995 10.175403 0.2829655 2 6 intracellular sterol transport
116 GO:0006595 0.0292995 10.175403 0.2829655 2 6 polyamine metabolic process
117 GO:0006596 0.0292995 10.175403 0.2829655 2 6 polyamine biosynthetic process
118 GO:0009064 0.0309536 5.100202 0.7074137 3 15 glutamine family amino acid metabolic process
119 GO:0006643 0.0315157 3.103278 1.7921147 5 38 membrane lipid metabolic process
120 GO:0019216 0.0360606 3.554613 1.2733447 4 27 regulation of lipid metabolic process
121 GO:0009084 0.0397595 8.138710 0.3301264 2 7 glutamine family amino acid biosynthetic process
122 GO:0045494 0.0397595 8.138710 0.3301264 2 7 photoreceptor cell maintenance
123 GO:0006767 0.0397595 8.138710 0.3301264 2 7 water-soluble vitamin metabolic process
124 GO:0048047 0.0471609 Inf 0.0471609 1 1 mating behavior, sex discrimination
125 GO:0045924 0.0471609 Inf 0.0471609 1 1 regulation of female receptivity
126 GO:0045916 0.0471609 Inf 0.0471609 1 1 negative regulation of complement activation
127 GO:0045938 0.0471609 Inf 0.0471609 1 1 positive regulation of circadian sleep/wake cycle, sleep
128 GO:1904109 0.0471609 Inf 0.0471609 1 1 positive regulation of cholesterol import
129 GO:0060180 0.0471609 Inf 0.0471609 1 1 female mating behavior
130 GO:0042822 0.0471609 Inf 0.0471609 1 1 pyridoxal phosphate metabolic process
131 GO:0042823 0.0471609 Inf 0.0471609 1 1 pyridoxal phosphate biosynthetic process
132 GO:0042573 0.0471609 Inf 0.0471609 1 1 retinoic acid metabolic process
133 GO:0046497 0.0471609 Inf 0.0471609 1 1 nicotinate nucleotide metabolic process
134 GO:0060620 0.0471609 Inf 0.0471609 1 1 regulation of cholesterol import
135 GO:0000103 0.0471609 Inf 0.0471609 1 1 sulfate assimilation
136 GO:0033344 0.0471609 Inf 0.0471609 1 1 cholesterol efflux
137 GO:0070508 0.0471609 Inf 0.0471609 1 1 cholesterol import
138 GO:0007621 0.0471609 Inf 0.0471609 1 1 negative regulation of female receptivity
139 GO:0043446 0.0471609 Inf 0.0471609 1 1 cellular alkane metabolic process
140 GO:0043447 0.0471609 Inf 0.0471609 1 1 alkane biosynthetic process
141 GO:2000258 0.0471609 Inf 0.0471609 1 1 negative regulation of protein activation cascade
142 GO:0010955 0.0471609 Inf 0.0471609 1 1 negative regulation of protein processing
143 GO:0002378 0.0471609 Inf 0.0471609 1 1 immunoglobulin biosynthetic process
144 GO:0019365 0.0471609 Inf 0.0471609 1 1 pyridine nucleotide salvage
145 GO:0019357 0.0471609 Inf 0.0471609 1 1 nicotinate nucleotide biosynthetic process
146 GO:0019358 0.0471609 Inf 0.0471609 1 1 nicotinate nucleotide salvage
147 GO:0019310 0.0471609 Inf 0.0471609 1 1 inositol catabolic process
148 GO:0019343 0.0471609 Inf 0.0471609 1 1 cysteine biosynthetic process via cystathionine
149 GO:0019344 0.0471609 Inf 0.0471609 1 1 cysteine biosynthetic process
150 GO:0009443 0.0471609 Inf 0.0471609 1 1 pyridoxal 5’-phosphate salvage
151 GO:1903318 0.0471609 Inf 0.0471609 1 1 negative regulation of protein maturation
152 GO:0002138 0.0471609 Inf 0.0471609 1 1 retinoic acid biosynthetic process
153 GO:0035376 0.0471609 Inf 0.0471609 1 1 sterol import
154 GO:0043606 0.0471609 Inf 0.0471609 1 1 formamide metabolic process
155 GO:2000911 0.0471609 Inf 0.0471609 1 1 positive regulation of sterol import
156 GO:2000909 0.0471609 Inf 0.0471609 1 1 regulation of sterol import
157 GO:0019852 0.0471609 Inf 0.0471609 1 1 L-ascorbic acid metabolic process
158 GO:0019556 0.0471609 Inf 0.0471609 1 1 histidine catabolic process to glutamate and formamide
159 GO:0008295 0.0471609 Inf 0.0471609 1 1 spermidine biosynthetic process
160 GO:0008216 0.0471609 Inf 0.0471609 1 1 spermidine metabolic process
161 GO:0032380 0.0471609 Inf 0.0471609 1 1 regulation of intracellular sterol transport
162 GO:0032382 0.0471609 Inf 0.0471609 1 1 positive regulation of intracellular sterol transport
163 GO:0032383 0.0471609 Inf 0.0471609 1 1 regulation of intracellular cholesterol transport
164 GO:0032385 0.0471609 Inf 0.0471609 1 1 positive regulation of intracellular cholesterol transport
165 GO:0032373 0.0471609 Inf 0.0471609 1 1 positive regulation of sterol transport
166 GO:0032376 0.0471609 Inf 0.0471609 1 1 positive regulation of cholesterol transport
167 GO:0032377 0.0471609 Inf 0.0471609 1 1 regulation of intracellular lipid transport
168 GO:0032379 0.0471609 Inf 0.0471609 1 1 positive regulation of intracellular lipid transport
169 GO:0016102 0.0471609 Inf 0.0471609 1 1 diterpenoid biosynthetic process
170 GO:0034699 0.0471609 Inf 0.0471609 1 1 response to luteinizing hormone
171 GO:0006535 0.0471609 Inf 0.0471609 1 1 cysteine biosynthetic process from serine
Module 6
GO_term_red <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_red.csv")
GO_term_red %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0006412 0.0000318 4.194114 3.9675533 14 239 translation
2 GO:0043043 0.0000366 4.136439 4.0173552 14 242 peptide biosynthetic process
3 GO:0043604 0.0000652 3.903106 4.2331636 14 255 amide biosynthetic process
4 GO:0043603 0.0001179 3.500972 5.0465950 15 304 cellular amide metabolic process
5 GO:0006518 0.0001258 3.648333 4.4987738 14 271 peptide metabolic process
6 GO:0045833 0.0002725 Inf 0.0332013 2 2 negative regulation of lipid metabolic process
7 GO:0016032 0.0034029 7.253501 0.6308244 4 38 viral process
8 GO:0019079 0.0041085 10.787543 0.3320128 3 20 viral genome replication
9 GO:1901566 0.0041428 2.266955 8.5493303 17 515 organonitrogen compound biosynthetic process
10 GO:0009267 0.0047363 10.186274 0.3486135 3 21 cellular response to starvation
11 GO:0031669 0.0054189 9.648297 0.3652141 3 22 cellular response to nutrient levels
12 GO:0031668 0.0061578 9.164118 0.3818148 3 23 cellular response to extracellular stimulus
13 GO:0044403 0.0062901 6.006969 0.7470289 4 45 symbiont process
14 GO:0044419 0.0073434 5.725360 0.7802301 4 47 interspecies interaction between organisms
15 GO:0010467 0.0081218 1.781539 21.5476325 32 1298 gene expression
16 GO:0071496 0.0107316 7.324235 0.4648180 3 28 cellular response to external stimulus
17 GO:0019058 0.0107316 7.324235 0.4648180 3 28 viral life cycle
18 GO:0046916 0.0135963 13.447028 0.1826071 2 11 cellular transition metal ion homeostasis
19 GO:0048507 0.0161410 12.100000 0.1992077 2 12 meristem development
20 GO:0000724 0.0161410 12.100000 0.1992077 2 12 double-strand break repair via homologous recombination
21 GO:0000725 0.0161410 12.100000 0.1992077 2 12 recombinational repair
22 GO:0038158 0.0166006 Inf 0.0166006 1 1 granulocyte colony-stimulating factor signaling pathway
23 GO:0044828 0.0166006 Inf 0.0166006 1 1 negative regulation by host of viral genome replication
24 GO:1904398 0.0166006 Inf 0.0166006 1 1 positive regulation of neuromuscular junction development
25 GO:0045953 0.0166006 Inf 0.0166006 1 1 negative regulation of natural killer cell mediated cytotoxicity
26 GO:0032692 0.0166006 Inf 0.0166006 1 1 negative regulation of interleukin-1 production
27 GO:0006924 0.0166006 Inf 0.0166006 1 1 activation-induced cell death of T cells
28 GO:0044528 0.0166006 Inf 0.0166006 1 1 regulation of mitochondrial mRNA stability
29 GO:0050819 0.0166006 Inf 0.0166006 1 1 negative regulation of coagulation
30 GO:0055108 0.0166006 Inf 0.0166006 1 1 Golgi to transport vesicle transport
31 GO:0048341 0.0166006 Inf 0.0166006 1 1 paraxial mesoderm formation
32 GO:0048305 0.0166006 Inf 0.0166006 1 1 immunoglobulin secretion
33 GO:0050995 0.0166006 Inf 0.0166006 1 1 negative regulation of lipid catabolic process
34 GO:0070341 0.0166006 Inf 0.0166006 1 1 fat cell proliferation
35 GO:0070342 0.0166006 Inf 0.0166006 1 1 brown fat cell proliferation
36 GO:0070344 0.0166006 Inf 0.0166006 1 1 regulation of fat cell proliferation
37 GO:0070345 0.0166006 Inf 0.0166006 1 1 negative regulation of fat cell proliferation
38 GO:0070347 0.0166006 Inf 0.0166006 1 1 regulation of brown fat cell proliferation
39 GO:0070348 0.0166006 Inf 0.0166006 1 1 negative regulation of brown fat cell proliferation
40 GO:0007110 0.0166006 Inf 0.0166006 1 1 meiosis I cytokinesis
41 GO:0048521 0.0166006 Inf 0.0166006 1 1 negative regulation of behavior
42 GO:0048541 0.0166006 Inf 0.0166006 1 1 Peyer’s patch development
43 GO:0048537 0.0166006 Inf 0.0166006 1 1 mucosal-associated lymphoid tissue development
44 GO:0070230 0.0166006 Inf 0.0166006 1 1 positive regulation of lymphocyte apoptotic process
45 GO:0070234 0.0166006 Inf 0.0166006 1 1 positive regulation of T cell apoptotic process
46 GO:0070235 0.0166006 Inf 0.0166006 1 1 regulation of activation-induced cell death of T cells
47 GO:0070237 0.0166006 Inf 0.0166006 1 1 positive regulation of activation-induced cell death of T cells
48 GO:0010152 0.0166006 Inf 0.0166006 1 1 pollen maturation
49 GO:0046851 0.0166006 Inf 0.0166006 1 1 negative regulation of bone remodeling
50 GO:0070836 0.0166006 Inf 0.0166006 1 1 caveola assembly
51 GO:2001212 0.0166006 Inf 0.0166006 1 1 regulation of vasculogenesis
52 GO:2001214 0.0166006 Inf 0.0166006 1 1 positive regulation of vasculogenesis
53 GO:0090330 0.0166006 Inf 0.0166006 1 1 regulation of platelet aggregation
54 GO:0090331 0.0166006 Inf 0.0166006 1 1 negative regulation of platelet aggregation
55 GO:0001911 0.0166006 Inf 0.0166006 1 1 negative regulation of leukocyte mediated cytotoxicity
56 GO:0046641 0.0166006 Inf 0.0166006 1 1 positive regulation of alpha-beta T cell proliferation
57 GO:0031342 0.0166006 Inf 0.0166006 1 1 negative regulation of cell killing
58 GO:0010543 0.0166006 Inf 0.0166006 1 1 regulation of platelet activation
59 GO:0010544 0.0166006 Inf 0.0166006 1 1 negative regulation of platelet activation
60 GO:0015761 0.0166006 Inf 0.0166006 1 1 mannose transmembrane transport
61 GO:2000108 0.0166006 Inf 0.0166006 1 1 positive regulation of leukocyte apoptotic process
62 GO:2000252 0.0166006 Inf 0.0166006 1 1 negative regulation of feeding behavior
63 GO:0019085 0.0166006 Inf 0.0166006 1 1 early viral transcription
64 GO:0019086 0.0166006 Inf 0.0166006 1 1 late viral transcription
65 GO:0000957 0.0166006 Inf 0.0166006 1 1 mitochondrial RNA catabolic process
66 GO:0000958 0.0166006 Inf 0.0166006 1 1 mitochondrial mRNA catabolic process
67 GO:0002347 0.0166006 Inf 0.0166006 1 1 response to tumor cell
68 GO:2000563 0.0166006 Inf 0.0166006 1 1 positive regulation of CD4-positive, alpha-beta T cell proliferation
69 GO:0030195 0.0166006 Inf 0.0166006 1 1 negative regulation of blood coagulation
70 GO:0002420 0.0166006 Inf 0.0166006 1 1 natural killer cell mediated cytotoxicity directed against tumor cell target
71 GO:0002423 0.0166006 Inf 0.0166006 1 1 natural killer cell mediated immune response to tumor cell
72 GO:0002418 0.0166006 Inf 0.0166006 1 1 immune response to tumor cell
73 GO:0035457 0.0166006 Inf 0.0166006 1 1 cellular response to interferon-alpha
74 GO:0002716 0.0166006 Inf 0.0166006 1 1 negative regulation of natural killer cell mediated immunity
75 GO:0030851 0.0166006 Inf 0.0166006 1 1 granulocyte differentiation
76 GO:0030852 0.0166006 Inf 0.0166006 1 1 regulation of granulocyte differentiation
77 GO:0030853 0.0166006 Inf 0.0166006 1 1 negative regulation of granulocyte differentiation
78 GO:0002704 0.0166006 Inf 0.0166006 1 1 negative regulation of leukocyte mediated immunity
79 GO:0002707 0.0166006 Inf 0.0166006 1 1 negative regulation of lymphocyte mediated immunity
80 GO:0120126 0.0166006 Inf 0.0166006 1 1 response to copper ion starvation
81 GO:0006067 0.0166006 Inf 0.0166006 1 1 ethanol metabolic process
82 GO:0006069 0.0166006 Inf 0.0166006 1 1 ethanol oxidation
83 GO:0009846 0.0166006 Inf 0.0166006 1 1 pollen germination
84 GO:0002855 0.0166006 Inf 0.0166006 1 1 regulation of natural killer cell mediated immune response to tumor cell
85 GO:0002856 0.0166006 Inf 0.0166006 1 1 negative regulation of natural killer cell mediated immune response to tumor cell
86 GO:0002858 0.0166006 Inf 0.0166006 1 1 regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
87 GO:0002859 0.0166006 Inf 0.0166006 1 1 negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
88 GO:0018343 0.0166006 Inf 0.0166006 1 1 protein farnesylation
89 GO:0002834 0.0166006 Inf 0.0166006 1 1 regulation of response to tumor cell
90 GO:0002835 0.0166006 Inf 0.0166006 1 1 negative regulation of response to tumor cell
91 GO:0002837 0.0166006 Inf 0.0166006 1 1 regulation of immune response to tumor cell
92 GO:0002838 0.0166006 Inf 0.0166006 1 1 negative regulation of immune response to tumor cell
93 GO:0051055 0.0166006 Inf 0.0166006 1 1 negative regulation of lipid biosynthetic process
94 GO:0051023 0.0166006 Inf 0.0166006 1 1 regulation of immunoglobulin secretion
95 GO:0051024 0.0166006 Inf 0.0166006 1 1 positive regulation of immunoglobulin secretion
96 GO:0035726 0.0166006 Inf 0.0166006 1 1 common myeloid progenitor cell proliferation
97 GO:1900047 0.0166006 Inf 0.0166006 1 1 negative regulation of hemostasis
98 GO:0035874 0.0166006 Inf 0.0166006 1 1 cellular response to copper ion starvation
99 GO:1901143 0.0166006 Inf 0.0166006 1 1 insulin catabolic process
100 GO:0034111 0.0166006 Inf 0.0166006 1 1 negative regulation of homotypic cell-cell adhesion
101 GO:0034104 0.0166006 Inf 0.0166006 1 1 negative regulation of tissue remodeling
102 GO:0045779 0.0166006 Inf 0.0166006 1 1 negative regulation of bone resorption
103 GO:0044342 0.0166006 Inf 0.0166006 1 1 type B pancreatic cell proliferation
104 GO:0045887 0.0166006 Inf 0.0166006 1 1 positive regulation of synaptic growth at neuromuscular junction
105 GO:0055069 0.0166006 Inf 0.0166006 1 1 zinc ion homeostasis
106 GO:0061469 0.0166006 Inf 0.0166006 1 1 regulation of type B pancreatic cell proliferation
107 GO:0032703 0.0166006 Inf 0.0166006 1 1 negative regulation of interleukin-2 production
108 GO:0044793 0.0166006 Inf 0.0166006 1 1 negative regulation by host of viral process
109 GO:0044091 0.0188719 10.997886 0.2158083 2 13 membrane biogenesis
110 GO:0060548 0.0210832 3.390706 1.5936616 5 96 negative regulation of cell death
111 GO:0007009 0.0217823 10.079457 0.2324090 2 14 plasma membrane organization
112 GO:0055076 0.0217823 10.079457 0.2324090 2 14 transition metal ion homeostasis
113 GO:0042594 0.0262791 5.075490 0.6474250 3 39 response to starvation
114 GO:0008643 0.0281153 8.636213 0.2656103 2 16 carbohydrate transport
115 GO:0007034 0.0299384 4.806502 0.6806263 3 41 vacuolar transport
116 GO:0006310 0.0299384 4.806502 0.6806263 3 41 DNA recombination
117 GO:0044854 0.0329288 59.908046 0.0332013 1 2 plasma membrane raft assembly
118 GO:0044857 0.0329288 59.908046 0.0332013 1 2 plasma membrane raft organization
119 GO:1904313 0.0329288 59.908046 0.0332013 1 2 response to methamphetamine hydrochloride
120 GO:0032663 0.0329288 59.908046 0.0332013 1 2 regulation of interleukin-2 production
121 GO:0032652 0.0329288 59.908046 0.0332013 1 2 regulation of interleukin-1 production
122 GO:0032623 0.0329288 59.908046 0.0332013 1 2 interleukin-2 production
123 GO:0032612 0.0329288 59.908046 0.0332013 1 2 interleukin-1 production
124 GO:0042149 0.0329288 59.908046 0.0332013 1 2 cellular response to glucose starvation
125 GO:0050850 0.0329288 59.908046 0.0332013 1 2 positive regulation of calcium-mediated signaling
126 GO:0050818 0.0329288 59.908046 0.0332013 1 2 regulation of coagulation
127 GO:0042267 0.0329288 59.908046 0.0332013 1 2 natural killer cell mediated cytotoxicity
128 GO:0042269 0.0329288 59.908046 0.0332013 1 2 regulation of natural killer cell mediated cytotoxicity
129 GO:0071353 0.0329288 59.908046 0.0332013 1 2 cellular response to interleukin-4
130 GO:0071359 0.0329288 59.908046 0.0332013 1 2 cellular response to dsRNA
131 GO:0048340 0.0329288 59.908046 0.0332013 1 2 paraxial mesoderm morphogenesis
132 GO:0070070 0.0329288 59.908046 0.0332013 1 2 proton-transporting V-type ATPase complex assembly
133 GO:0070072 0.0329288 59.908046 0.0332013 1 2 vacuolar proton-transporting V-type ATPase complex assembly
134 GO:0071287 0.0329288 59.908046 0.0332013 1 2 cellular response to manganese ion
135 GO:0010042 0.0329288 59.908046 0.0332013 1 2 response to manganese ion
136 GO:0048867 0.0329288 59.908046 0.0332013 1 2 stem cell fate determination
137 GO:0070231 0.0329288 59.908046 0.0332013 1 2 T cell apoptotic process
138 GO:0070232 0.0329288 59.908046 0.0332013 1 2 regulation of T cell apoptotic process
139 GO:2001185 0.0329288 59.908046 0.0332013 1 2 regulation of CD8-positive, alpha-beta T cell activation
140 GO:2001187 0.0329288 59.908046 0.0332013 1 2 positive regulation of CD8-positive, alpha-beta T cell activation
141 GO:0090324 0.0329288 59.908046 0.0332013 1 2 negative regulation of oxidative phosphorylation
142 GO:0070670 0.0329288 59.908046 0.0332013 1 2 response to interleukin-4
143 GO:2000345 0.0329288 59.908046 0.0332013 1 2 regulation of hepatocyte proliferation
144 GO:2000346 0.0329288 59.908046 0.0332013 1 2 negative regulation of hepatocyte proliferation
145 GO:0046640 0.0329288 59.908046 0.0332013 1 2 regulation of alpha-beta T cell proliferation
146 GO:0046633 0.0329288 59.908046 0.0332013 1 2 alpha-beta T cell proliferation
147 GO:0021589 0.0329288 59.908046 0.0332013 1 2 cerebellum structural organization
148 GO:0021577 0.0329288 59.908046 0.0332013 1 2 hindbrain structural organization
149 GO:0043331 0.0329288 59.908046 0.0332013 1 2 response to dsRNA
150 GO:0030026 0.0329288 59.908046 0.0332013 1 2 cellular manganese ion homeostasis
151 GO:0019054 0.0329288 59.908046 0.0332013 1 2 modulation by virus of host process
152 GO:0019080 0.0329288 59.908046 0.0332013 1 2 viral gene expression
153 GO:0019083 0.0329288 59.908046 0.0332013 1 2 viral transcription
154 GO:0019048 0.0329288 59.908046 0.0332013 1 2 modulation by virus of host morphology or physiology
155 GO:0090503 0.0329288 59.908046 0.0332013 1 2 RNA phosphodiester bond hydrolysis, exonucleolytic
156 GO:2000561 0.0329288 59.908046 0.0332013 1 2 regulation of CD4-positive, alpha-beta T cell proliferation
157 GO:0030193 0.0329288 59.908046 0.0332013 1 2 regulation of blood coagulation
158 GO:0002228 0.0329288 59.908046 0.0332013 1 2 natural killer cell mediated immunity
159 GO:0002761 0.0329288 59.908046 0.0332013 1 2 regulation of myeloid leukocyte differentiation
160 GO:0002762 0.0329288 59.908046 0.0332013 1 2 negative regulation of myeloid leukocyte differentiation
161 GO:0002715 0.0329288 59.908046 0.0332013 1 2 regulation of natural killer cell mediated immunity
162 GO:0072574 0.0329288 59.908046 0.0332013 1 2 hepatocyte proliferation
163 GO:0072575 0.0329288 59.908046 0.0332013 1 2 epithelial cell proliferation involved in liver morphogenesis
164 GO:0072576 0.0329288 59.908046 0.0332013 1 2 liver morphogenesis
165 GO:0016036 0.0329288 59.908046 0.0332013 1 2 cellular response to phosphate starvation
166 GO:1903894 0.0329288 59.908046 0.0332013 1 2 regulation of IRE1-mediated unfolded protein response
167 GO:0035739 0.0329288 59.908046 0.0332013 1 2 CD4-positive, alpha-beta T cell proliferation
168 GO:1900046 0.0329288 59.908046 0.0332013 1 2 regulation of hemostasis
169 GO:0002637 0.0329288 59.908046 0.0332013 1 2 regulation of immunoglobulin production
170 GO:0002639 0.0329288 59.908046 0.0332013 1 2 positive regulation of immunoglobulin production
171 GO:1901142 0.0329288 59.908046 0.0332013 1 2 insulin metabolic process
172 GO:0044068 0.0329288 59.908046 0.0332013 1 2 modulation by symbiont of host cellular process
173 GO:0016338 0.0329288 59.908046 0.0332013 1 2 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules
174 GO:0034110 0.0329288 59.908046 0.0332013 1 2 regulation of homotypic cell-cell adhesion
175 GO:0044003 0.0329288 59.908046 0.0332013 1 2 modification by symbiont of host morphology or physiology
176 GO:0061045 0.0329288 59.908046 0.0332013 1 2 negative regulation of wound healing
177 GO:1990090 0.0329288 59.908046 0.0332013 1 2 cellular response to nerve growth factor stimulus
178 GO:1990089 0.0329288 59.908046 0.0332013 1 2 response to nerve growth factor
179 GO:0055071 0.0329288 59.908046 0.0332013 1 2 manganese ion homeostasis
180 GO:0045670 0.0329288 59.908046 0.0332013 1 2 regulation of osteoclast differentiation
181 GO:0045671 0.0329288 59.908046 0.0332013 1 2 negative regulation of osteoclast differentiation
182 GO:0045601 0.0329288 59.908046 0.0332013 1 2 regulation of endothelial cell differentiation
183 GO:1901998 0.0329288 59.908046 0.0332013 1 2 toxin transport
184 GO:0036037 0.0329288 59.908046 0.0332013 1 2 CD8-positive, alpha-beta T cell activation
185 GO:0051962 0.0359055 4.452224 0.7304282 3 44 positive regulation of nervous system development
186 GO:0031032 0.0359055 4.452224 0.7304282 3 44 actomyosin structure organization
187 GO:0010941 0.0366111 2.594235 2.4734956 6 149 regulation of cell death
188 GO:0050678 0.0388018 7.108071 0.3154122 2 19 regulation of epithelial cell proliferation
189 GO:0045069 0.0388018 7.108071 0.3154122 2 19 regulation of viral genome replication
190 GO:0048524 0.0426566 6.711886 0.3320128 2 20 positive regulation of viral process
191 GO:0006414 0.0426566 6.711886 0.3320128 2 20 translational elongation
192 GO:0071345 0.0447408 4.053333 0.7968308 3 48 cellular response to cytokine stimulus
193 GO:0043066 0.0448827 3.176252 1.3446520 4 81 negative regulation of apoptotic process
194 GO:0034641 0.0449812 1.489675 28.0550840 36 1690 cellular nitrogen compound metabolic process
195 GO:0090501 0.0466482 6.357405 0.3486135 2 21 RNA phosphodiester bond hydrolysis
196 GO:0045980 0.0489888 29.948276 0.0498019 1 3 negative regulation of nucleotide metabolic process
197 GO:0006983 0.0489888 29.948276 0.0498019 1 3 ER overload response
198 GO:0042130 0.0489888 29.948276 0.0498019 1 3 negative regulation of T cell proliferation
199 GO:0042102 0.0489888 29.948276 0.0498019 1 3 positive regulation of T cell proliferation
200 GO:0036335 0.0489888 29.948276 0.0498019 1 3 intestinal stem cell homeostasis
201 GO:0048339 0.0489888 29.948276 0.0498019 1 3 paraxial mesoderm development
202 GO:0070071 0.0489888 29.948276 0.0498019 1 3 proton-transporting two-sector ATPase complex assembly
203 GO:0050672 0.0489888 29.948276 0.0498019 1 3 negative regulation of lymphocyte proliferation
204 GO:0032945 0.0489888 29.948276 0.0498019 1 3 negative regulation of mononuclear cell proliferation
205 GO:0036213 0.0489888 29.948276 0.0498019 1 3 contractile ring contraction
206 GO:0001765 0.0489888 29.948276 0.0498019 1 3 membrane raft assembly
207 GO:0048532 0.0489888 29.948276 0.0498019 1 3 anatomical structure arrangement
208 GO:0000212 0.0489888 29.948276 0.0498019 1 3 meiotic spindle organization
209 GO:0070664 0.0489888 29.948276 0.0498019 1 3 negative regulation of leukocyte proliferation
210 GO:0002082 0.0489888 29.948276 0.0498019 1 3 regulation of oxidative phosphorylation
211 GO:0043114 0.0489888 29.948276 0.0498019 1 3 regulation of vascular permeability
212 GO:0043116 0.0489888 29.948276 0.0498019 1 3 negative regulation of vascular permeability
213 GO:0000959 0.0489888 29.948276 0.0498019 1 3 mitochondrial RNA metabolic process
214 GO:0000916 0.0489888 29.948276 0.0498019 1 3 actomyosin contractile ring contraction
215 GO:1903035 0.0489888 29.948276 0.0498019 1 3 negative regulation of response to wounding
216 GO:0110111 0.0489888 29.948276 0.0498019 1 3 negative regulation of animal organ morphogenesis
217 GO:0002377 0.0489888 29.948276 0.0498019 1 3 immunoglobulin production
218 GO:2000516 0.0489888 29.948276 0.0498019 1 3 positive regulation of CD4-positive, alpha-beta T cell activation
219 GO:0031579 0.0489888 29.948276 0.0498019 1 3 membrane raft organization
220 GO:0035455 0.0489888 29.948276 0.0498019 1 3 response to interferon-alpha
221 GO:0035437 0.0489888 29.948276 0.0498019 1 3 maintenance of protein localization in endoplasmic reticulum
222 GO:0009856 0.0489888 29.948276 0.0498019 1 3 pollination
223 GO:1903579 0.0489888 29.948276 0.0498019 1 3 negative regulation of ATP metabolic process
224 GO:0045453 0.0489888 29.948276 0.0498019 1 3 bone resorption
225 GO:0045124 0.0489888 29.948276 0.0498019 1 3 regulation of bone resorption
226 GO:1900101 0.0489888 29.948276 0.0498019 1 3 regulation of endoplasmic reticulum unfolded protein response
227 GO:0055092 0.0489888 29.948276 0.0498019 1 3 sterol homeostasis
228 GO:1900543 0.0489888 29.948276 0.0498019 1 3 negative regulation of purine nucleotide metabolic process
Module 7
GO_term_black <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_black.csv")
GO_term_black %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0051127 0.0000000 193.308823 0.0662139 5 9 positive regulation of actin nucleation
2 GO:0051125 0.0000000 154.617647 0.0735710 5 10 regulation of actin nucleation
3 GO:0006030 0.0000000 30.891047 0.3237125 7 44 chitin metabolic process
4 GO:1901071 0.0000000 27.855945 0.3531409 7 48 glucosamine-containing compound metabolic process
5 GO:0006040 0.0000000 27.187500 0.3604980 7 49 amino sugar metabolic process
6 GO:0006022 0.0000001 24.804348 0.3899264 7 53 aminoglycan metabolic process
7 GO:0042752 0.0000002 51.441176 0.1471420 5 20 regulation of circadian rhythm
8 GO:0045010 0.0000004 45.371972 0.1618563 5 22 actin nucleation
9 GO:0030838 0.0000008 38.544118 0.1839276 5 25 positive regulation of actin filament polymerization
10 GO:0007623 0.0000029 28.513072 0.2354273 5 32 circadian rhythm
11 GO:0030833 0.0000039 26.536511 0.2501415 5 34 regulation of actin filament polymerization
12 GO:0030041 0.0000046 25.647059 0.2574986 5 35 actin filament polymerization
13 GO:0008064 0.0000053 24.814991 0.2648557 5 36 regulation of actin polymerization or depolymerization
14 GO:0030832 0.0000053 24.814991 0.2648557 5 36 regulation of actin filament length
15 GO:0032273 0.0000079 22.612457 0.2869270 5 39 positive regulation of protein polymerization
16 GO:0008154 0.0000090 21.962185 0.2942841 5 40 actin polymerization or depolymerization
17 GO:0110053 0.0000115 20.767091 0.3089983 5 42 regulation of actin filament organization
18 GO:0031334 0.0000146 19.694570 0.3237125 5 44 positive regulation of protein complex assembly
19 GO:1902905 0.0000163 19.198529 0.3310696 5 45 positive regulation of supramolecular fiber organization
20 GO:0051495 0.0000225 17.848837 0.3531409 5 48 positive regulation of cytoskeleton organization
21 GO:0032271 0.0000225 17.848837 0.3531409 5 48 regulation of protein polymerization
22 GO:0032956 0.0000249 17.439840 0.3604980 5 49 regulation of actin cytoskeleton organization
23 GO:0048511 0.0000275 17.049020 0.3678551 5 50 rhythmic process
24 GO:0032535 0.0000440 15.329412 0.4046406 5 55 regulation of cellular component size
25 GO:0043254 0.0000524 14.734163 0.4193548 5 57 regulation of protein complex assembly
26 GO:0051258 0.0000672 13.922460 0.4414261 5 60 protein polymerization
27 GO:0032970 0.0000729 13.671219 0.4487832 5 61 regulation of actin filament-based process
28 GO:1902903 0.0000852 13.194726 0.4634975 5 63 regulation of supramolecular fiber organization
29 GO:0007015 0.0000919 12.968594 0.4708546 5 64 actin filament organization
30 GO:0090066 0.0001065 12.538573 0.4855688 5 66 regulation of anatomical structure size
31 GO:0051493 0.0001412 11.757919 0.5149972 5 70 regulation of cytoskeleton organization
32 GO:0044089 0.0002220 10.600490 0.5664969 5 77 positive regulation of cellular component biogenesis
33 GO:0017144 0.0002469 6.592271 1.2948500 7 176 drug metabolic process
34 GO:0010638 0.0006506 8.264067 0.7136389 5 97 positive regulation of organelle organization
35 GO:0008152 0.0009875 4.337692 26.1397849 35 3553 metabolic process
36 GO:0006629 0.0010122 4.557309 2.1335597 8 290 lipid metabolic process
37 GO:0097435 0.0016386 6.640867 0.8754952 5 119 supramolecular fiber organization
38 GO:0044087 0.0021852 6.195757 0.9343520 5 127 regulation of cellular component biogenesis
39 GO:1901135 0.0022360 3.985484 2.4131296 8 328 carbohydrate derivative metabolic process
40 GO:0030036 0.0022619 6.144189 0.9417091 5 128 actin cytoskeleton organization
41 GO:0030029 0.0023405 6.093453 0.9490662 5 129 actin filament-based process
42 GO:0045892 0.0023405 6.093453 0.9490662 5 129 negative regulation of transcription, DNA-templated
43 GO:1902679 0.0025038 5.994398 0.9637804 5 131 negative regulation of RNA biosynthetic process
44 GO:1903507 0.0025038 5.994398 0.9637804 5 131 negative regulation of nucleic acid-templated transcription
45 GO:0051253 0.0025884 5.946040 0.9711375 5 132 negative regulation of RNA metabolic process
46 GO:2000113 0.0033428 5.584967 1.0299943 5 140 negative regulation of cellular macromolecule biosynthetic process
47 GO:0045934 0.0035539 5.501288 1.0447085 5 142 negative regulation of nucleobase-containing compound metabolic process
48 GO:0007010 0.0036576 4.578019 1.5229202 6 207 cytoskeleton organization
49 GO:0010558 0.0037745 5.420017 1.0594228 5 144 negative regulation of macromolecule biosynthetic process
50 GO:0031327 0.0042451 5.264295 1.0888512 5 148 negative regulation of cellular biosynthetic process
51 GO:0009890 0.0046247 5.153102 1.1109225 5 151 negative regulation of biosynthetic process
52 GO:0051130 0.0047564 5.117047 1.1182796 5 152 positive regulation of cellular component organization
53 GO:0006869 0.0063447 8.865646 0.3825693 3 52 lipid transport
54 GO:0033043 0.0074284 4.571377 1.2433503 5 169 regulation of organelle organization
55 GO:0010876 0.0107844 7.225000 0.4634975 3 63 lipid localization
56 GO:0034622 0.0120041 4.035771 1.3978495 5 190 cellular protein-containing complex assembly
57 GO:0010629 0.0141661 3.862389 1.4567063 5 198 negative regulation of gene expression
58 GO:0090210 0.0146615 138.447368 0.0147142 1 2 regulation of establishment of blood-brain barrier
59 GO:0090212 0.0146615 138.447368 0.0147142 1 2 negative regulation of establishment of blood-brain barrier
60 GO:0051452 0.0146615 138.447368 0.0147142 1 2 intracellular pH reduction
61 GO:0045851 0.0146615 138.447368 0.0147142 1 2 pH reduction
62 GO:0042360 0.0146615 138.447368 0.0147142 1 2 vitamin E metabolic process
63 GO:0050912 0.0219134 69.210526 0.0220713 1 3 detection of chemical stimulus involved in sensory perception of taste
64 GO:0050907 0.0219134 69.210526 0.0220713 1 3 detection of chemical stimulus involved in sensory perception
65 GO:0035337 0.0219134 69.210526 0.0220713 1 3 fatty-acyl-CoA metabolic process
66 GO:0009593 0.0219134 69.210526 0.0220713 1 3 detection of chemical stimulus
67 GO:0051180 0.0219134 69.210526 0.0220713 1 3 vitamin transport
68 GO:0051172 0.0241893 3.338633 1.6700623 5 227 negative regulation of nitrogen compound metabolic process
69 GO:0065003 0.0280504 3.202827 1.7362762 5 236 protein-containing complex assembly
70 GO:0031324 0.0280504 3.202827 1.7362762 5 236 negative regulation of cellular metabolic process
71 GO:0060856 0.0291134 46.131579 0.0294284 1 4 establishment of blood-brain barrier
72 GO:0051453 0.0291134 46.131579 0.0294284 1 4 regulation of intracellular pH
73 GO:0065008 0.0312557 2.568326 3.0899830 7 420 regulation of biological quality
74 GO:0030004 0.0362617 34.592105 0.0367855 1 5 cellular monovalent inorganic cation homeostasis
75 GO:0120009 0.0362617 34.592105 0.0367855 1 5 intermembrane lipid transfer
76 GO:0030641 0.0362617 34.592105 0.0367855 1 5 regulation of cellular pH
77 GO:0071704 0.0369178 1.998812 23.1307301 29 3144 organic substance metabolic process
78 GO:0000209 0.0394076 6.883322 0.3163554 2 43 protein polyubiquitination
79 GO:0009268 0.0433587 27.668421 0.0441426 1 6 response to pH
80 GO:0043933 0.0461176 2.773030 1.9864177 5 270 protein-containing complex subunit organization
81 GO:0010605 0.0498979 2.708379 2.0305603 5 276 negative regulation of macromolecule metabolic process
Module 9
GO_term_magenta <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_magenta.csv")
GO_term_magenta %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0046034 0.0000000 75.565217 0.4708546 16 64 ATP metabolic process
2 GO:0009205 0.0000000 71.079284 0.4929259 16 67 purine ribonucleoside triphosphate metabolic process
3 GO:0009199 0.0000000 69.698997 0.5002830 16 68 ribonucleoside triphosphate metabolic process
4 GO:0009144 0.0000000 68.370796 0.5076401 16 69 purine nucleoside triphosphate metabolic process
5 GO:0009167 0.0000000 64.670807 0.5297114 16 72 purine ribonucleoside monophosphate metabolic process
6 GO:0009126 0.0000000 64.670807 0.5297114 16 72 purine nucleoside monophosphate metabolic process
7 GO:0009141 0.0000000 63.524028 0.5370685 16 73 nucleoside triphosphate metabolic process
8 GO:0009161 0.0000000 61.347089 0.5517827 16 75 ribonucleoside monophosphate metabolic process
9 GO:0009123 0.0000000 60.313043 0.5591398 16 76 nucleoside monophosphate metabolic process
10 GO:0009150 0.0000000 42.369309 0.7430673 16 101 purine ribonucleotide metabolic process
11 GO:0009259 0.0000000 41.379310 0.7577816 16 103 ribonucleotide metabolic process
12 GO:0006163 0.0000000 39.529861 0.7872100 16 107 purine nucleotide metabolic process
13 GO:0019693 0.0000000 39.092628 0.7945671 16 108 ribose phosphate metabolic process
14 GO:0072521 0.0000000 36.279315 0.8460668 16 115 purine-containing compound metabolic process
15 GO:0017144 0.0000000 27.688969 1.2948500 18 176 drug metabolic process
16 GO:0009117 0.0000000 27.035573 1.0888512 16 148 nucleotide metabolic process
17 GO:0006753 0.0000000 26.419324 1.1109225 16 151 nucleoside phosphate metabolic process
18 GO:0055086 0.0000000 21.489328 1.3316355 16 181 nucleobase-containing small molecule metabolic process
19 GO:0006754 0.0000000 74.871429 0.2207131 9 30 ATP biosynthetic process
20 GO:0009145 0.0000000 68.334783 0.2354273 9 32 purine nucleoside triphosphate biosynthetic process
21 GO:0009206 0.0000000 68.334783 0.2354273 9 32 purine ribonucleoside triphosphate biosynthetic process
22 GO:0009142 0.0000000 65.475000 0.2427844 9 33 nucleoside triphosphate biosynthetic process
23 GO:0009201 0.0000000 65.475000 0.2427844 9 33 ribonucleoside triphosphate biosynthetic process
24 GO:0019637 0.0000000 15.689179 1.9422750 17 264 organophosphate metabolic process
25 GO:0022904 0.0000000 96.737327 0.1618563 8 22 respiratory electron transport chain
26 GO:0006119 0.0000000 90.270968 0.1692134 8 23 oxidative phosphorylation
27 GO:0015985 0.0000000 164.218750 0.1029994 7 14 energy coupled proton transport, down electrochemical gradient
28 GO:0015986 0.0000000 164.218750 0.1029994 7 14 ATP synthesis coupled proton transport
29 GO:0009168 0.0000000 56.078571 0.2722128 9 37 purine ribonucleoside monophosphate biosynthetic process
30 GO:0009127 0.0000000 56.078571 0.2722128 9 37 purine nucleoside monophosphate biosynthetic process
31 GO:0009156 0.0000000 52.320000 0.2869270 9 39 ribonucleoside monophosphate biosynthetic process
32 GO:0009124 0.0000000 50.622581 0.2942841 9 40 nucleoside monophosphate biosynthetic process
33 GO:0022900 0.0000000 71.212224 0.1986418 8 27 electron transport chain
34 GO:0045333 0.0000000 46.129412 0.3163554 9 43 cellular respiration
35 GO:1901135 0.0000000 12.301520 2.4131296 17 328 carbohydrate derivative metabolic process
36 GO:0042773 0.0000000 95.703125 0.1397849 7 19 ATP synthesis coupled electron transport
37 GO:0006091 0.0000000 29.400791 0.5223543 10 71 generation of precursor metabolites and energy
38 GO:0015980 0.0000000 36.411628 0.3825693 9 52 energy derivation by oxidation of organic compounds
39 GO:0009152 0.0000000 32.587500 0.4193548 9 57 purine ribonucleotide biosynthetic process
40 GO:0046390 0.0000000 31.272000 0.4340690 9 59 ribose phosphate biosynthetic process
41 GO:0009260 0.0000000 31.272000 0.4340690 9 59 ribonucleotide biosynthetic process
42 GO:0006164 0.0000000 30.652941 0.4414261 9 60 purine nucleotide biosynthetic process
43 GO:0072522 0.0000000 28.933333 0.4634975 9 63 purine-containing compound biosynthetic process
44 GO:0044281 0.0000000 9.535220 3.3254103 18 452 small molecule metabolic process
45 GO:0042775 0.0000000 106.121212 0.1103565 6 15 mitochondrial ATP synthesis coupled electron transport
46 GO:1902600 0.0000000 47.742188 0.2280702 7 31 proton transmembrane transport
47 GO:0009165 0.0000000 20.748000 0.6179966 9 84 nucleotide biosynthetic process
48 GO:1901293 0.0000000 20.748000 0.6179966 9 84 nucleoside phosphate biosynthetic process
49 GO:0090407 0.0000000 13.506186 1.0373514 10 141 organophosphate biosynthetic process
50 GO:0055114 0.0000001 8.667247 2.2071307 13 300 oxidation-reduction process
51 GO:0098662 0.0000001 17.847742 0.6106395 8 83 inorganic cation transmembrane transport
52 GO:0098660 0.0000001 17.151365 0.6327108 8 86 inorganic ion transmembrane transport
53 GO:0098655 0.0000005 14.188058 0.7504244 8 102 cation transmembrane transport
54 GO:1901137 0.0000006 10.023645 1.3610640 10 185 carbohydrate derivative biosynthetic process
55 GO:0006796 0.0000008 5.549513 5.3118280 18 722 phosphate-containing compound metabolic process
56 GO:0006793 0.0000009 5.504332 5.3486135 18 727 phosphorus metabolic process
57 GO:0015672 0.0000060 12.292799 0.7283531 7 99 monovalent inorganic cation transport
58 GO:0034220 0.0000219 8.282410 1.2286361 8 167 ion transmembrane transport
59 GO:0006120 0.0000300 73.000000 0.0662139 3 9 mitochondrial electron transport, NADH to ubiquinone
60 GO:0006812 0.0001248 6.366011 1.5670628 8 213 cation transport
61 GO:0006122 0.0001575 284.378378 0.0220713 2 3 mitochondrial electron transport, ubiquinol to cytochrome c
62 GO:1901566 0.0008748 3.708759 3.7889078 11 515 organonitrogen compound biosynthetic process
63 GO:0006811 0.0030153 3.783410 2.5308432 8 344 ion transport
64 GO:0032981 0.0039090 25.803440 0.0956423 2 13 mitochondrial respiratory chain complex I assembly
65 GO:0010257 0.0039090 25.803440 0.0956423 2 13 NADH dehydrogenase complex assembly
66 GO:0055085 0.0047344 3.247416 3.3401245 9 454 transmembrane transport
67 GO:0007005 0.0047444 6.567619 0.6915676 4 94 mitochondrion organization
68 GO:0033108 0.0066904 18.908108 0.1250707 2 17 mitochondrial respiratory chain complex assembly
69 GO:0006139 0.0072839 2.353025 10.4691568 18 1423 nucleobase-containing compound metabolic process
70 GO:1902957 0.0073571 Inf 0.0073571 1 1 negative regulation of mitochondrial electron transport, NADH to ubiquinone
71 GO:0006123 0.0073571 Inf 0.0073571 1 1 mitochondrial electron transport, cytochrome c to oxygen
72 GO:1901856 0.0073571 Inf 0.0073571 1 1 negative regulation of cellular respiration
73 GO:1905447 0.0073571 Inf 0.0073571 1 1 negative regulation of mitochondrial ATP synthesis coupled electron transport
74 GO:0009060 0.0101412 14.916074 0.1544992 2 21 aerobic respiration
75 GO:0046483 0.0102690 2.253399 10.8002264 18 1468 heterocycle metabolic process
76 GO:0006725 0.0103454 2.251255 10.8075835 18 1469 cellular aromatic compound metabolic process
77 GO:1901564 0.0129385 2.162080 12.8234295 20 1743 organonitrogen compound metabolic process
78 GO:1901360 0.0137145 2.169894 11.0945105 18 1508 organic cyclic compound metabolic process
79 GO:0090324 0.0146615 138.447368 0.0147142 1 2 negative regulation of oxidative phosphorylation
80 GO:1902956 0.0146615 138.447368 0.0147142 1 2 regulation of mitochondrial electron transport, NADH to ubiquinone
81 GO:0019646 0.0146615 138.447368 0.0147142 1 2 aerobic electron transport chain
82 GO:1905446 0.0146615 138.447368 0.0147142 1 2 regulation of mitochondrial ATP synthesis coupled electron transport
83 GO:0032780 0.0146615 138.447368 0.0147142 1 2 negative regulation of ATPase activity
84 GO:0016310 0.0160223 2.773042 3.3548387 8 456 phosphorylation
85 GO:0034641 0.0205583 2.041562 12.4335031 19 1690 cellular nitrogen compound metabolic process
86 GO:0006936 0.0214425 9.753961 0.2280702 2 31 muscle contraction
87 GO:0045980 0.0219134 69.210526 0.0220713 1 3 negative regulation of nucleotide metabolic process
88 GO:0002082 0.0219134 69.210526 0.0220713 1 3 regulation of oxidative phosphorylation
89 GO:2000983 0.0219134 69.210526 0.0220713 1 3 regulation of ATP citrate synthase activity
90 GO:2000984 0.0219134 69.210526 0.0220713 1 3 negative regulation of ATP citrate synthase activity
91 GO:1903579 0.0219134 69.210526 0.0220713 1 3 negative regulation of ATP metabolic process
92 GO:0055070 0.0219134 69.210526 0.0220713 1 3 copper ion homeostasis
93 GO:0006662 0.0219134 69.210526 0.0220713 1 3 glycerol ether metabolic process
94 GO:0018904 0.0219134 69.210526 0.0220713 1 3 ether metabolic process
95 GO:1900543 0.0219134 69.210526 0.0220713 1 3 negative regulation of purine nucleotide metabolic process
96 GO:0030150 0.0291134 46.131579 0.0294284 1 4 protein import into mitochondrial matrix
97 GO:0035434 0.0291134 46.131579 0.0294284 1 4 copper ion transmembrane transport
98 GO:0003012 0.0345109 7.431010 0.2942841 2 40 muscle system process
99 GO:0062014 0.0362617 34.592105 0.0367855 1 5 negative regulation of small molecule metabolic process
100 GO:0043457 0.0362617 34.592105 0.0367855 1 5 regulation of cellular respiration
101 GO:1900037 0.0362617 34.592105 0.0367855 1 5 regulation of cellular response to hypoxia
102 GO:0006825 0.0362617 34.592105 0.0367855 1 5 copper ion transport
103 GO:0048793 0.0433587 27.668421 0.0441426 1 6 pronephros development
104 GO:0055065 0.0463204 6.266667 0.3457838 2 47 metal ion homeostasis
105 GO:0044057 0.0481140 6.129260 0.3531409 2 48 regulation of system process
Module 10
GO_term_purple <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_purple.csv")
GO_term_purple %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0070527 0.0000000 101.389961 0.0950764 5 12 platelet aggregation
2 GO:0030168 0.0000000 88.699324 0.1029994 5 13 platelet activation
3 GO:0034109 0.0000000 88.699324 0.1029994 5 13 homotypic cell-cell adhesion
4 GO:0050817 0.0000001 64.471744 0.1267685 5 16 coagulation
5 GO:0007596 0.0000001 64.471744 0.1267685 5 16 blood coagulation
6 GO:0007599 0.0000001 64.471744 0.1267685 5 16 hemostasis
7 GO:0009612 0.0000001 33.544872 0.2535371 6 32 response to mechanical stimulus
8 GO:0030029 0.0000005 11.679545 1.0220713 9 129 actin filament-based process
9 GO:0050878 0.0000006 41.669316 0.1743067 5 22 regulation of body fluid levels
10 GO:0030036 0.0000055 10.076471 1.0141483 8 128 actin cytoskeleton organization
11 GO:0098974 0.0000091 134.769231 0.0475382 3 6 postsynaptic actin cytoskeleton organization
12 GO:0099188 0.0000091 134.769231 0.0475382 3 6 postsynaptic cytoskeleton organization
13 GO:0035902 0.0000091 134.769231 0.0475382 3 6 response to immobilization stress
14 GO:0071257 0.0000158 101.057692 0.0554612 3 7 cellular response to electrical stimulus
15 GO:0002121 0.0000158 101.057692 0.0554612 3 7 inter-male aggressive behavior
16 GO:1903920 0.0000158 101.057692 0.0554612 3 7 positive regulation of actin filament severing
17 GO:1903919 0.0000158 101.057692 0.0554612 3 7 negative regulation of actin filament severing
18 GO:0035995 0.0000158 101.057692 0.0554612 3 7 detection of muscle stretch
19 GO:0055003 0.0000158 101.057692 0.0554612 3 7 cardiac myofibril assembly
20 GO:1904030 0.0000158 101.057692 0.0554612 3 7 negative regulation of cyclin-dependent protein kinase activity
21 GO:0048857 0.0000252 80.830769 0.0633843 3 8 neural nucleus development
22 GO:0021762 0.0000252 80.830769 0.0633843 3 8 substantia nigra development
23 GO:0002118 0.0000252 80.830769 0.0633843 3 8 aggressive behavior
24 GO:0016319 0.0000252 80.830769 0.0633843 3 8 mushroom body development
25 GO:1903918 0.0000252 80.830769 0.0633843 3 8 regulation of actin filament severing
26 GO:0045663 0.0000252 80.830769 0.0633843 3 8 positive regulation of myoblast differentiation
27 GO:0042060 0.0000293 16.785714 0.3723826 5 47 wound healing
28 GO:0007291 0.0000376 67.346154 0.0713073 3 9 sperm individualization
29 GO:0010831 0.0000376 67.346154 0.0713073 3 9 positive regulation of myotube differentiation
30 GO:0014897 0.0000376 67.346154 0.0713073 3 9 striated muscle hypertrophy
31 GO:0051014 0.0000376 67.346154 0.0713073 3 9 actin filament severing
32 GO:0035994 0.0000376 67.346154 0.0713073 3 9 response to muscle stretch
33 GO:0055013 0.0000376 67.346154 0.0713073 3 9 cardiac muscle cell development
34 GO:0045662 0.0000376 67.346154 0.0713073 3 9 negative regulation of myoblast differentiation
35 GO:0003300 0.0000376 67.346154 0.0713073 3 9 cardiac muscle hypertrophy
36 GO:0051091 0.0000382 26.255639 0.1980758 4 25 positive regulation of DNA-binding transcription factor activity
37 GO:0043044 0.0000534 57.714286 0.0792303 3 10 ATP-dependent chromatin remodeling
38 GO:0090175 0.0000534 57.714286 0.0792303 3 10 regulation of establishment of planar polarity
39 GO:0002026 0.0000534 57.714286 0.0792303 3 10 regulation of the force of heart contraction
40 GO:0014896 0.0000534 57.714286 0.0792303 3 10 muscle hypertrophy
41 GO:0030901 0.0000534 57.714286 0.0792303 3 10 midbrain development
42 GO:0050982 0.0000730 50.490385 0.0871534 3 11 detection of mechanical stimulus
43 GO:0007349 0.0000730 50.490385 0.0871534 3 11 cellularization
44 GO:0010830 0.0000730 50.490385 0.0871534 3 11 regulation of myotube differentiation
45 GO:0051155 0.0000730 50.490385 0.0871534 3 11 positive regulation of striated muscle cell differentiation
46 GO:0051149 0.0000730 50.490385 0.0871534 3 11 positive regulation of muscle cell differentiation
47 GO:0055006 0.0000730 50.490385 0.0871534 3 11 cardiac cell development
48 GO:0060048 0.0000730 50.490385 0.0871534 3 11 cardiac muscle contraction
49 GO:0009611 0.0000755 13.531705 0.4516129 5 57 response to wounding
50 GO:0006874 0.0000804 21.186235 0.2376910 4 30 cellular calcium ion homeostasis
51 GO:0006936 0.0000918 20.397661 0.2456140 4 31 muscle contraction
52 GO:0072503 0.0000918 20.397661 0.2456140 4 31 cellular divalent inorganic cation homeostasis
53 GO:0001974 0.0000968 44.871795 0.0950764 3 12 blood vessel remodeling
54 GO:0032091 0.0000968 44.871795 0.0950764 3 12 negative regulation of protein binding
55 GO:0051602 0.0000968 44.871795 0.0950764 3 12 response to electrical stimulus
56 GO:0051090 0.0001043 19.665413 0.2535371 4 32 regulation of DNA-binding transcription factor activity
57 GO:0055074 0.0001043 19.665413 0.2535371 4 32 calcium ion homeostasis
58 GO:0042592 0.0001127 6.417457 1.5370685 8 194 homeostatic process
59 GO:0001775 0.0001224 12.117894 0.4991511 5 63 cell activation
60 GO:0032507 0.0001252 40.376923 0.1029994 3 13 maintenance of protein location in cell
61 GO:0051651 0.0001252 40.376923 0.1029994 3 13 maintenance of location in cell
62 GO:0072507 0.0001492 17.752122 0.2773062 4 35 divalent inorganic cation homeostasis
63 GO:0006941 0.0001585 36.699301 0.1109225 3 14 striated muscle contraction
64 GO:0045445 0.0001585 36.699301 0.1109225 3 14 myoblast differentiation
65 GO:0051153 0.0001585 36.699301 0.1109225 3 14 regulation of striated muscle cell differentiation
66 GO:0045661 0.0001585 36.699301 0.1109225 3 14 regulation of myoblast differentiation
67 GO:0007010 0.0001771 5.982856 1.6400679 8 207 cytoskeleton organization
68 GO:0052646 0.0001829 262.900000 0.0237691 2 3 alditol phosphate metabolic process
69 GO:0006072 0.0001829 262.900000 0.0237691 2 3 glycerol-3-phosphate metabolic process
70 GO:0001895 0.0001970 33.634615 0.1188455 3 15 retina homeostasis
71 GO:0045214 0.0001970 33.634615 0.1188455 3 15 sarcomere organization
72 GO:0051147 0.0001970 33.634615 0.1188455 3 15 regulation of muscle cell differentiation
73 GO:0055007 0.0001970 33.634615 0.1188455 3 15 cardiac muscle cell differentiation
74 GO:0000281 0.0002411 31.041420 0.1267685 3 16 mitotic cytokinesis
75 GO:0014902 0.0002411 31.041420 0.1267685 3 16 myotube differentiation
76 GO:0045185 0.0002411 31.041420 0.1267685 3 16 maintenance of protein location
77 GO:0051100 0.0002411 31.041420 0.1267685 3 16 negative regulation of binding
78 GO:1904029 0.0002411 31.041420 0.1267685 3 16 regulation of cyclin-dependent protein kinase activity
79 GO:0003012 0.0002531 15.271930 0.3169213 4 40 muscle system process
80 GO:0006811 0.0002629 4.607972 2.7255235 10 344 ion transport
81 GO:0006875 0.0002788 14.856330 0.3248444 4 41 cellular metal ion homeostasis
82 GO:0051705 0.0002912 28.818681 0.1346916 3 17 multi-organism behavior
83 GO:1905330 0.0002912 28.818681 0.1346916 3 17 regulation of morphogenesis of an epithelium
84 GO:0009628 0.0003585 6.136145 1.3706848 7 173 response to abiotic stimulus
85 GO:0031032 0.0003674 13.734210 0.3486135 4 44 actomyosin structure organization
86 GO:0030003 0.0004009 13.396662 0.3565365 4 45 cellular cation homeostasis
87 GO:0006873 0.0004009 13.396662 0.3565365 4 45 cellular ion homeostasis
88 GO:0035051 0.0004104 25.206731 0.1505376 3 19 cardiocyte differentiation
89 GO:0055065 0.0004745 12.768666 0.3723826 4 47 metal ion homeostasis
90 GO:0048771 0.0004801 23.719457 0.1584607 3 20 tissue remodeling
91 GO:0099173 0.0004801 23.719457 0.1584607 3 20 postsynapse organization
92 GO:0044057 0.0005147 12.476077 0.3803056 4 48 regulation of system process
93 GO:0001736 0.0005571 22.397436 0.1663837 3 21 establishment of planar polarity
94 GO:0098609 0.0005594 8.531641 0.6893039 5 87 cell-cell adhesion
95 GO:0055082 0.0006022 11.929062 0.3961517 4 50 cellular chemical homeostasis
96 GO:0061983 0.0006037 87.600000 0.0396152 2 5 meiosis II cell cycle process
97 GO:0007111 0.0006037 87.600000 0.0396152 2 5 meiosis II cytokinesis
98 GO:0033206 0.0006037 87.600000 0.0396152 2 5 meiotic cytokinesis
99 GO:0061640 0.0006415 21.214575 0.1743067 3 22 cytoskeleton-dependent cytokinesis
100 GO:0001738 0.0006415 21.214575 0.1743067 3 22 morphogenesis of a polarized epithelium
101 GO:0007164 0.0006415 21.214575 0.1743067 3 22 establishment of tissue polarity
102 GO:0048646 0.0006769 6.473485 1.0933786 6 138 anatomical structure formation involved in morphogenesis
103 GO:0051179 0.0006939 2.906479 10.0860215 20 1273 localization
104 GO:0035148 0.0007337 20.150000 0.1822298 3 23 tube formation
105 GO:0006469 0.0007337 20.150000 0.1822298 3 23 negative regulation of protein kinase activity
106 GO:0008016 0.0008339 19.186813 0.1901528 3 24 regulation of heart contraction
107 GO:0065009 0.0008710 4.636406 2.0758347 8 262 regulation of molecular function
108 GO:0006796 0.0008784 3.213983 5.7204301 14 722 phosphate-containing compound metabolic process
109 GO:0098771 0.0009280 10.540486 0.4436899 4 56 inorganic ion homeostasis
110 GO:0055080 0.0009280 10.540486 0.4436899 4 56 cation homeostasis
111 GO:0006793 0.0009420 3.187938 5.7600453 14 727 phosphorus metabolic process
112 GO:2000027 0.0009424 18.311189 0.1980758 3 25 regulation of animal organ morphogenesis
113 GO:0043393 0.0009424 18.311189 0.1980758 3 25 regulation of protein binding
114 GO:0003015 0.0009424 18.311189 0.1980758 3 25 heart process
115 GO:0060047 0.0009424 18.311189 0.1980758 3 25 heart contraction
116 GO:0033673 0.0010594 17.511706 0.2059989 3 26 negative regulation of kinase activity
117 GO:0009581 0.0010594 17.511706 0.2059989 3 26 detection of external stimulus
118 GO:0009582 0.0010594 17.511706 0.2059989 3 26 detection of abiotic stimulus
119 GO:0009653 0.0010895 4.073554 2.6859083 9 339 anatomical structure morphogenesis
120 GO:0019725 0.0011053 7.267736 0.8002264 5 101 cellular homeostasis
121 GO:0030239 0.0011853 16.778846 0.2139219 3 27 myofibril assembly
122 GO:1903522 0.0011853 16.778846 0.2139219 3 27 regulation of blood circulation
123 GO:0032970 0.0012813 9.606648 0.4833050 4 61 regulation of actin filament-based process
124 GO:0048738 0.0013203 16.104615 0.2218449 3 28 cardiac muscle tissue development
125 GO:0032989 0.0014207 5.562092 1.2597623 6 159 cellular component morphogenesis
126 GO:0050801 0.0014459 9.277431 0.4991511 4 63 ion homeostasis
127 GO:0000910 0.0014645 15.482249 0.2297680 3 29 cytokinesis
128 GO:0006338 0.0014645 15.482249 0.2297680 3 29 chromatin remodeling
129 GO:0051348 0.0016183 14.905983 0.2376910 3 30 negative regulation of transferase activity
130 GO:0043086 0.0017197 8.823429 0.5229202 4 66 negative regulation of catalytic activity
131 GO:0071214 0.0017819 14.370879 0.2456140 3 31 cellular response to abiotic stimulus
132 GO:0001894 0.0017819 14.370879 0.2456140 3 31 tissue homeostasis
133 GO:0007519 0.0017819 14.370879 0.2456140 3 31 skeletal muscle tissue development
134 GO:0104004 0.0017819 14.370879 0.2456140 3 31 cellular response to environmental stimulus
135 GO:0034220 0.0018282 5.277433 1.3231466 6 167 ion transmembrane transport
136 GO:0007623 0.0019554 13.872679 0.2535371 3 32 circadian rhythm
137 GO:0051606 0.0019554 13.872679 0.2535371 3 32 detection of stimulus
138 GO:0060538 0.0021392 13.407692 0.2614601 3 33 skeletal muscle organ development
139 GO:0008015 0.0021392 13.407692 0.2614601 3 33 blood circulation
140 GO:0003013 0.0021392 13.407692 0.2614601 3 33 circulatory system process
141 GO:0055002 0.0021392 13.407692 0.2614601 3 33 striated muscle cell development
142 GO:0010927 0.0023333 12.972705 0.2693831 3 34 cellular component assembly involved in morphogenesis
143 GO:0051098 0.0023333 12.972705 0.2693831 3 34 regulation of binding
144 GO:0055001 0.0023333 12.972705 0.2693831 3 34 muscle cell development
145 GO:0006909 0.0025381 12.564904 0.2773062 3 35 phagocytosis
146 GO:0048871 0.0025381 12.564904 0.2773062 3 35 multicellular organismal homeostasis
147 GO:0051235 0.0025381 12.564904 0.2773062 3 35 maintenance of location
148 GO:0001523 0.0026492 32.818750 0.0792303 2 10 retinoid metabolic process
149 GO:0016101 0.0026492 32.818750 0.0792303 2 10 diterpenoid metabolic process
150 GO:0007286 0.0027536 12.181818 0.2852292 3 36 spermatid development
151 GO:0048515 0.0029802 11.821267 0.2931522 3 37 spermatid differentiation
152 GO:0046434 0.0032179 11.481319 0.3010753 3 38 organophosphate catabolic process
153 GO:0006721 0.0032217 29.166667 0.0871534 2 11 terpenoid metabolic process
154 GO:0006816 0.0034670 11.160256 0.3089983 3 39 calcium ion transport
155 GO:0045944 0.0036436 7.084074 0.6417657 4 81 positive regulation of transcription by RNA polymerase II
156 GO:0030001 0.0039688 5.331601 1.0696095 5 135 metal ion transport
157 GO:0044092 0.0039787 6.902065 0.6576118 4 83 negative regulation of molecular function
158 GO:0048878 0.0043341 6.729045 0.6734578 4 85 chemical homeostasis
159 GO:0006835 0.0045233 23.854545 0.1029994 2 13 dicarboxylic acid transport
160 GO:0051146 0.0045801 10.036539 0.3406904 3 43 striated muscle cell differentiation
161 GO:0060041 0.0045801 10.036539 0.3406904 3 43 retina development in camera-type eye
162 GO:0065008 0.0047661 3.216987 3.3276740 9 420 regulation of biological quality
163 GO:0001933 0.0048883 9.789869 0.3486135 3 44 negative regulation of protein phosphorylation
164 GO:0009887 0.0050734 5.014689 1.1329938 5 143 animal organ morphogenesis
165 GO:0070838 0.0052088 9.554945 0.3565365 3 45 divalent metal ion transport
166 GO:0072511 0.0052088 9.554945 0.3565365 3 45 divalent inorganic cation transport
167 GO:0030866 0.0052507 21.862500 0.1109225 2 14 cortical actin cytoskeleton organization
168 GO:0015849 0.0055418 9.330948 0.3644595 3 46 organic acid transport
169 GO:0046942 0.0055418 9.330948 0.3644595 3 46 carboxylic acid transport
170 GO:0007155 0.0057009 4.869623 1.1646859 5 147 cell adhesion
171 GO:0022610 0.0057009 4.869623 1.1646859 5 147 biological adhesion
172 GO:0042692 0.0058873 9.117133 0.3723826 3 47 muscle cell differentiation
173 GO:0030865 0.0060282 20.176923 0.1188455 2 15 cortical cytoskeleton organization
174 GO:0050808 0.0062454 8.912821 0.3803056 3 48 synapse organization
175 GO:0060249 0.0070003 8.530278 0.3961517 3 50 anatomical structure homeostasis
176 GO:0048511 0.0070003 8.530278 0.3961517 3 50 rhythmic process
177 GO:0042326 0.0073972 8.350962 0.4040747 3 51 negative regulation of phosphorylation
178 GO:0150063 0.0074394 5.721884 0.7843803 4 99 visual system development
179 GO:0048880 0.0074394 5.721884 0.7843803 4 99 sensory system development
180 GO:0001654 0.0074394 5.721884 0.7843803 4 99 eye development
181 GO:0055085 0.0079173 2.950357 3.5970572 9 454 transmembrane transport
182 GO:0046168 0.0079230 Inf 0.0079230 1 1 glycerol-3-phosphate catabolic process
183 GO:0035025 0.0079230 Inf 0.0079230 1 1 positive regulation of Rho protein signal transduction
184 GO:0006002 0.0079230 Inf 0.0079230 1 1 fructose 6-phosphate metabolic process
185 GO:0016310 0.0081434 2.935936 3.6129032 9 456 phosphorylation
186 GO:0009605 0.0083069 3.799397 1.7985286 6 227 response to external stimulus
187 GO:0045859 0.0086671 7.855204 0.4278438 3 54 regulation of protein kinase activity
188 GO:0034613 0.0087466 3.365424 2.3927561 7 302 cellular protein localization
189 GO:0051301 0.0091171 7.702663 0.4357668 3 55 cell division
190 GO:0006468 0.0092346 3.064471 3.0345218 8 383 protein phosphorylation
191 GO:0070727 0.0093757 3.317726 2.4244482 7 306 cellular macromolecule localization
192 GO:0048513 0.0095183 3.046965 3.0503679 8 385 animal organ development
193 GO:0014706 0.0095807 7.555878 0.4436899 3 56 striated muscle tissue development
194 GO:0015711 0.0100578 7.414530 0.4516129 3 57 organic anion transport
195 GO:0060537 0.0110531 7.146978 0.4674590 3 59 muscle tissue development
196 GO:0045936 0.0115715 7.020243 0.4753820 3 60 negative regulation of phosphate metabolic process
197 GO:0007517 0.0115715 7.020243 0.4753820 3 60 muscle organ development
198 GO:0010563 0.0115715 7.020243 0.4753820 3 60 negative regulation of phosphorus metabolic process
199 GO:0043549 0.0115715 7.020243 0.4753820 3 60 regulation of kinase activity
200 GO:1903508 0.0117498 4.973443 0.8953028 4 113 positive regulation of nucleic acid-templated transcription
201 GO:0045893 0.0117498 4.973443 0.8953028 4 113 positive regulation of transcription, DNA-templated
202 GO:0007283 0.0121038 6.897878 0.4833050 3 61 spermatogenesis
203 GO:1902680 0.0121080 4.927273 0.9032258 4 114 positive regulation of RNA biosynthetic process
204 GO:0043010 0.0126500 6.779661 0.4912281 3 62 camera-type eye development
205 GO:0007423 0.0136112 4.750693 0.9349179 4 118 sensory organ development
206 GO:0007409 0.0137844 6.554855 0.5070741 3 64 axonogenesis
207 GO:0009166 0.0139552 12.471429 0.1822298 2 23 nucleotide catabolic process
208 GO:0003333 0.0139552 12.471429 0.1822298 2 23 amino acid transmembrane transport
209 GO:0097435 0.0140048 4.708467 0.9428410 4 119 supramolecular fiber organization
210 GO:0033365 0.0148138 4.626181 0.9586870 4 121 protein localization to organelle
211 GO:0048232 0.0149753 6.344322 0.5229202 3 66 male gamete generation
212 GO:0000060 0.0157848 128.243902 0.0158461 1 2 protein import into nucleus, translocation
213 GO:0031288 0.0157848 128.243902 0.0158461 1 2 sorocarp morphogenesis
214 GO:0045596 0.0162230 6.146746 0.5387663 3 68 negative regulation of cell differentiation
215 GO:1901292 0.0163834 11.382609 0.1980758 2 25 nucleoside phosphate catabolic process
216 GO:0006865 0.0163834 11.382609 0.1980758 2 25 amino acid transport
217 GO:0010557 0.0165196 4.469769 0.9903792 4 125 positive regulation of macromolecule biosynthetic process
218 GO:0006810 0.0173709 2.142198 8.6994907 15 1098 transport
219 GO:0031400 0.0182017 5.872172 0.5625354 3 71 negative regulation of protein modification process
220 GO:0031328 0.0193032 4.253626 1.0379174 4 131 positive regulation of cellular biosynthetic process
221 GO:0051254 0.0197938 4.219572 1.0458404 4 132 positive regulation of RNA metabolic process
222 GO:0003006 0.0202921 4.186046 1.0537634 4 133 developmental process involved in reproduction
223 GO:0035023 0.0203367 10.063462 0.2218449 2 28 regulation of Rho protein signal transduction
224 GO:1903825 0.0203367 10.063462 0.2218449 2 28 organic acid transmembrane transport
225 GO:1905039 0.0203367 10.063462 0.2218449 2 28 carboxylic acid transmembrane transport
226 GO:0051338 0.0210411 5.541667 0.5942275 3 75 regulation of transferase activity
227 GO:0006720 0.0217346 9.688889 0.2297680 2 29 isoprenoid metabolic process
228 GO:0061564 0.0217870 5.464700 0.6021505 3 76 axon development
229 GO:0048667 0.0217870 5.464700 0.6021505 3 76 cell morphogenesis involved in neuron differentiation
230 GO:0007281 0.0217870 5.464700 0.6021505 3 76 germ cell development
231 GO:0006897 0.0217870 5.464700 0.6021505 3 76 endocytosis
232 GO:0051234 0.0221567 2.067125 8.9451047 15 1129 establishment of localization
233 GO:0009891 0.0223633 4.056985 1.0854556 4 137 positive regulation of biosynthetic process
234 GO:0007507 0.0225473 5.389813 0.6100736 3 77 heart development
235 GO:0032975 0.0235857 64.109756 0.0237691 1 3 amino acid transmembrane import into vacuole
236 GO:0046579 0.0235857 64.109756 0.0237691 1 3 positive regulation of Ras protein signal transduction
237 GO:0015802 0.0235857 64.109756 0.0237691 1 3 basic amino acid transport
238 GO:0051057 0.0235857 64.109756 0.0237691 1 3 positive regulation of small GTPase mediated signal transduction
239 GO:0034486 0.0235857 64.109756 0.0237691 1 3 vacuolar transmembrane transport
240 GO:0006820 0.0241113 5.245951 0.6259196 3 79 anion transport
241 GO:0048468 0.0241985 2.952550 2.2739106 6 287 cell development
242 GO:0007266 0.0246466 9.017241 0.2456140 2 31 Rho protein signal transduction
243 GO:0032502 0.0247864 2.219088 5.8313526 11 736 developmental process
244 GO:0006812 0.0253625 3.281575 1.6876061 5 213 cation transport
245 GO:0022603 0.0257332 5.109468 0.6417657 3 81 regulation of anatomical structure morphogenesis
246 GO:1903046 0.0261594 8.715000 0.2535371 2 32 meiotic cell cycle process
247 GO:0045935 0.0268851 3.820829 1.1488398 4 145 positive regulation of nucleobase-containing compound metabolic process
248 GO:0022412 0.0274128 4.979808 0.6576118 3 83 cellular process involved in reproduction in multicellular organism
249 GO:0045597 0.0274128 4.979808 0.6576118 3 83 positive regulation of cell differentiation
250 GO:0098657 0.0274128 4.979808 0.6576118 3 83 import into cell
251 GO:0034404 0.0277091 8.432258 0.2614601 2 33 nucleobase-containing small molecule biosynthetic process
252 GO:0048858 0.0291501 4.856473 0.6734578 3 85 cell projection morphogenesis
253 GO:0048812 0.0291501 4.856473 0.6734578 3 85 neuron projection morphogenesis
254 GO:0002009 0.0291501 4.856473 0.6734578 3 85 morphogenesis of an epithelium
255 GO:0120039 0.0291501 4.856473 0.6734578 3 85 plasma membrane bounded cell projection morphogenesis
256 GO:0051093 0.0291501 4.856473 0.6734578 3 85 negative regulation of developmental process
257 GO:0044093 0.0293389 3.712523 1.1805320 4 149 positive regulation of molecular function
258 GO:0008104 0.0297878 2.582540 3.0503679 7 385 protein localization
259 GO:0035239 0.0300403 4.797034 0.6813809 3 86 tube morphogenesis
260 GO:0015729 0.0313262 42.731707 0.0316921 1 4 oxaloacetate transport
261 GO:0010628 0.0325896 3.585263 1.2201471 4 154 positive regulation of gene expression
262 GO:0048856 0.0326248 2.181335 5.3005093 10 669 anatomical structure development
263 GO:0032990 0.0337449 4.572944 0.7130730 3 90 cell part morphogenesis
264 GO:0051321 0.0342644 7.462857 0.2931522 2 37 meiotic cell cycle
265 GO:0098656 0.0342644 7.462857 0.2931522 2 37 anion transmembrane transport
266 GO:0048729 0.0386968 4.320234 0.7526882 3 95 tissue morphogenesis
267 GO:0043090 0.0390069 32.042683 0.0396152 1 5 amino acid import
268 GO:0046578 0.0395377 6.869737 0.3169213 2 40 regulation of Ras protein signal transduction
269 GO:0030154 0.0396081 2.416418 3.2405207 7 409 cell differentiation
270 GO:0000904 0.0397296 4.272953 0.7606112 3 96 cell morphogenesis involved in differentiation
271 GO:0040011 0.0427890 3.270218 1.3310696 4 168 locomotion
272 GO:0007610 0.0429124 4.137019 0.7843803 3 99 behavior
273 GO:0007420 0.0440013 4.093577 0.7923033 3 100 brain development
274 GO:0061061 0.0451041 4.051020 0.8002264 3 101 muscle structure development
275 GO:0003008 0.0451865 3.209581 1.3548387 4 171 system process
276 GO:0050896 0.0452893 1.827112 10.6247878 16 1341 response to stimulus
277 GO:0032269 0.0462207 4.009324 0.8081494 3 102 negative regulation of cellular protein metabolic process
278 GO:0098655 0.0462207 4.009324 0.8081494 3 102 cation transmembrane transport
279 GO:0015740 0.0466280 25.629268 0.0475382 1 6 C4-dicarboxylate transport
280 GO:0015804 0.0466280 25.629268 0.0475382 1 6 neutral amino acid transport
281 GO:0009642 0.0466280 25.629268 0.0475382 1 6 response to light intensity
282 GO:0048869 0.0472384 2.316268 3.3672892 7 425 cellular developmental process
283 GO:0060322 0.0473511 3.968462 0.8160724 3 103 head development
284 GO:0048731 0.0488350 2.176815 4.1279004 8 521 system development
285 GO:0072359 0.0496530 3.889140 0.8319185 3 105 circulatory system development
286 GO:0035295 0.0496530 3.889140 0.8319185 3 105 tube development
Module 13
GO_term_salmon <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_salmon.csv")
GO_term_salmon %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0055114 0.0000000 37.504152 1.5846067 19 300 oxidation-reduction process
2 GO:0006091 0.0000000 66.279661 0.3750236 12 71 generation of precursor metabolites and energy
3 GO:0006099 0.0000000 263.250000 0.0845124 8 16 tricarboxylic acid cycle
4 GO:0006101 0.0000000 233.955556 0.0897944 8 17 citrate metabolic process
5 GO:0072350 0.0000000 191.345454 0.1003584 8 19 tricarboxylic acid metabolic process
6 GO:0009060 0.0000000 161.846154 0.1109225 8 21 aerobic respiration
7 GO:0016999 0.0000000 131.425000 0.1267685 8 24 antibiotic metabolic process
8 GO:0045333 0.0000000 72.989164 0.2271270 9 43 cellular respiration
9 GO:0015980 0.0000000 57.613219 0.2746652 9 52 energy derivation by oxidation of organic compounds
10 GO:0017144 0.0000000 20.031372 0.9296359 11 176 drug metabolic process
11 GO:0019752 0.0000000 14.701968 1.0669685 10 202 carboxylic acid metabolic process
12 GO:0043436 0.0000000 14.544674 1.0775325 10 204 oxoacid metabolic process
13 GO:0006082 0.0000000 14.544674 1.0775325 10 204 organic acid metabolic process
14 GO:0044281 0.0000001 9.543204 2.3874741 13 452 small molecule metabolic process
15 GO:0032981 0.0000364 63.156000 0.0686663 3 13 mitochondrial respiratory chain complex I assembly
16 GO:0010257 0.0000364 63.156000 0.0686663 3 13 NADH dehydrogenase complex assembly
17 GO:0033108 0.0000854 45.077143 0.0897944 3 17 mitochondrial respiratory chain complex assembly
18 GO:0022900 0.0003547 26.245000 0.1426146 3 27 electron transport chain
19 GO:0065002 0.0034844 26.964103 0.0897944 2 17 intracellular protein transmembrane transport
20 GO:0006090 0.0034844 26.964103 0.0897944 2 17 pyruvate metabolic process
21 GO:0016052 0.0039071 25.274038 0.0950764 2 18 carbohydrate catabolic process
22 GO:0046034 0.0044337 10.253115 0.3380494 3 64 ATP metabolic process
23 GO:0009205 0.0050442 9.766875 0.3538955 3 67 purine ribonucleoside triphosphate metabolic process
24 GO:0009199 0.0052585 9.614769 0.3591775 3 68 ribonucleoside triphosphate metabolic process
25 GO:0060317 0.0052820 Inf 0.0052820 1 1 cardiac epithelial to mesenchymal transition
26 GO:0051930 0.0052820 Inf 0.0052820 1 1 regulation of sensory perception of pain
27 GO:0071787 0.0052820 Inf 0.0052820 1 1 endoplasmic reticulum tubular network formation
28 GO:0048755 0.0052820 Inf 0.0052820 1 1 branching morphogenesis of a nerve
29 GO:0070571 0.0052820 Inf 0.0052820 1 1 negative regulation of neuron projection regeneration
30 GO:0021801 0.0052820 Inf 0.0052820 1 1 cerebral cortex radial glia guided migration
31 GO:0021553 0.0052820 Inf 0.0052820 1 1 olfactory nerve development
32 GO:2000172 0.0052820 Inf 0.0052820 1 1 regulation of branching morphogenesis of a nerve
33 GO:0033598 0.0052820 Inf 0.0052820 1 1 mammary gland epithelial cell proliferation
34 GO:0033599 0.0052820 Inf 0.0052820 1 1 regulation of mammary gland epithelial cell proliferation
35 GO:0033601 0.0052820 Inf 0.0052820 1 1 positive regulation of mammary gland epithelial cell proliferation
36 GO:0033603 0.0052820 Inf 0.0052820 1 1 positive regulation of dopamine secretion
37 GO:0033605 0.0052820 Inf 0.0052820 1 1 positive regulation of catecholamine secretion
38 GO:0022030 0.0052820 Inf 0.0052820 1 1 telencephalon glial cell migration
39 GO:0008347 0.0052820 Inf 0.0052820 1 1 glial cell migration
40 GO:0006007 0.0052820 Inf 0.0052820 1 1 glucose catabolic process
41 GO:1901475 0.0052820 Inf 0.0052820 1 1 pyruvate transmembrane transport
42 GO:0006850 0.0052820 Inf 0.0052820 1 1 mitochondrial pyruvate transmembrane transport
43 GO:0006848 0.0052820 Inf 0.0052820 1 1 pyruvate transport
44 GO:0045687 0.0052820 Inf 0.0052820 1 1 positive regulation of glial cell differentiation
45 GO:1990542 0.0053105 21.271255 0.1109225 2 21 mitochondrial transmembrane transport
46 GO:0009144 0.0054782 9.467273 0.3644595 3 69 purine nucleoside triphosphate metabolic process
47 GO:0009167 0.0061702 9.050435 0.3803056 3 72 purine ribonucleoside monophosphate metabolic process
48 GO:0009126 0.0061702 9.050435 0.3803056 3 72 purine nucleoside monophosphate metabolic process
49 GO:0009141 0.0064120 8.919429 0.3855876 3 73 nucleoside triphosphate metabolic process
50 GO:0008152 0.0066579 4.121788 18.7670251 25 3553 metabolic process
51 GO:0030308 0.0069117 18.360140 0.1267685 2 24 negative regulation of cell growth
52 GO:0009161 0.0069126 8.668333 0.3961517 3 75 ribonucleoside monophosphate metabolic process
53 GO:0009123 0.0071714 8.547945 0.4014337 3 76 nucleoside monophosphate metabolic process
54 GO:0071806 0.0100030 14.945869 0.1531786 2 29 protein transmembrane transport
55 GO:0051954 0.0105371 195.259259 0.0105640 1 2 positive regulation of amine transport
56 GO:0051931 0.0105371 195.259259 0.0105640 1 2 regulation of sensory perception
57 GO:0046365 0.0105371 195.259259 0.0105640 1 2 monosaccharide catabolic process
58 GO:0021795 0.0105371 195.259259 0.0105640 1 2 cerebral cortex cell migration
59 GO:0021799 0.0105371 195.259259 0.0105640 1 2 cerebral cortex radially oriented cell migration
60 GO:0021885 0.0105371 195.259259 0.0105640 1 2 forebrain cell migration
61 GO:0021545 0.0105371 195.259259 0.0105640 1 2 cranial nerve development
62 GO:0019320 0.0105371 195.259259 0.0105640 1 2 hexose catabolic process
63 GO:0022029 0.0105371 195.259259 0.0105640 1 2 telencephalon cell migration
64 GO:0045685 0.0105371 195.259259 0.0105640 1 2 regulation of glial cell differentiation
65 GO:0006754 0.0106827 14.409341 0.1584607 2 30 ATP biosynthetic process
66 GO:0045926 0.0113824 13.909814 0.1637427 2 31 negative regulation of growth
67 GO:0009145 0.0121018 13.443590 0.1690247 2 32 purine nucleoside triphosphate biosynthetic process
68 GO:0009206 0.0121018 13.443590 0.1690247 2 32 purine ribonucleoside triphosphate biosynthetic process
69 GO:0007005 0.0128352 6.833407 0.4965101 3 94 mitochondrion organization
70 GO:0009142 0.0128408 13.007444 0.1743067 2 33 nucleoside triphosphate biosynthetic process
71 GO:0009201 0.0128408 13.007444 0.1743067 2 33 ribonucleoside triphosphate biosynthetic process
72 GO:0009150 0.0155699 6.336735 0.5334842 3 101 purine ribonucleotide metabolic process
73 GO:2001025 0.0157655 97.611111 0.0158461 1 3 positive regulation of response to drug
74 GO:0014059 0.0157655 97.611111 0.0158461 1 3 regulation of dopamine secretion
75 GO:0014046 0.0157655 97.611111 0.0158461 1 3 dopamine secretion
76 GO:0006108 0.0157655 97.611111 0.0158461 1 3 malate metabolic process
77 GO:0050432 0.0157655 97.611111 0.0158461 1 3 catecholamine secretion
78 GO:0050433 0.0157655 97.611111 0.0158461 1 3 regulation of catecholamine secretion
79 GO:0061180 0.0157655 97.611111 0.0158461 1 3 mammary gland epithelium development
80 GO:0009168 0.0159879 11.512088 0.1954348 2 37 purine ribonucleoside monophosphate biosynthetic process
81 GO:0009127 0.0159879 11.512088 0.1954348 2 37 purine nucleoside monophosphate biosynthetic process
82 GO:0009259 0.0164074 6.207600 0.5440483 3 103 ribonucleotide metabolic process
83 GO:0001558 0.0176733 10.885655 0.2059989 2 39 regulation of cell growth
84 GO:0009156 0.0176733 10.885655 0.2059989 2 39 ribonucleoside monophosphate biosynthetic process
85 GO:0006163 0.0181579 5.964231 0.5651764 3 107 purine nucleotide metabolic process
86 GO:0009124 0.0185433 10.597166 0.2112809 2 40 nucleoside monophosphate biosynthetic process
87 GO:0019693 0.0186113 5.906286 0.5704584 3 108 ribose phosphate metabolic process
88 GO:0051937 0.0209672 65.061728 0.0211281 1 4 catecholamine transport
89 GO:0014015 0.0209672 65.061728 0.0211281 1 4 positive regulation of gliogenesis
90 GO:0021675 0.0209672 65.061728 0.0211281 1 4 nerve development
91 GO:0015872 0.0209672 65.061728 0.0211281 1 4 dopamine transport
92 GO:0043280 0.0209672 65.061728 0.0211281 1 4 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
93 GO:0030517 0.0209672 65.061728 0.0211281 1 4 negative regulation of axon extension
94 GO:0072521 0.0219628 5.529643 0.6074326 3 115 purine-containing compound metabolic process
95 GO:0051952 0.0261423 48.787037 0.0264101 1 5 regulation of amine transport
96 GO:0071300 0.0261423 48.787037 0.0264101 1 5 cellular response to retinoic acid
97 GO:0071786 0.0261423 48.787037 0.0264101 1 5 endoplasmic reticulum tubular network organization
98 GO:0015837 0.0261423 48.787037 0.0264101 1 5 amine transport
99 GO:0045039 0.0261423 48.787037 0.0264101 1 5 protein import into mitochondrial inner membrane
100 GO:0016049 0.0303228 8.035385 0.2746652 2 52 cell growth
101 GO:2001056 0.0312911 39.022222 0.0316921 1 6 positive regulation of cysteine-type endopeptidase activity
102 GO:0046323 0.0312911 39.022222 0.0316921 1 6 glucose import
103 GO:0046324 0.0312911 39.022222 0.0316921 1 6 regulation of glucose import
104 GO:0070570 0.0312911 39.022222 0.0316921 1 6 regulation of neuron projection regeneration
105 GO:0014013 0.0312911 39.022222 0.0316921 1 6 regulation of gliogenesis
106 GO:0015844 0.0312911 39.022222 0.0316921 1 6 monoamine transport
107 GO:0030879 0.0312911 39.022222 0.0316921 1 6 mammary gland development
108 GO:0005975 0.0345276 4.602090 0.7236370 3 137 carbohydrate metabolic process
109 GO:0009152 0.0359127 7.297902 0.3010753 2 57 purine ribonucleotide biosynthetic process
110 GO:0050771 0.0364137 32.512346 0.0369742 1 7 negative regulation of axonogenesis
111 GO:0050679 0.0364137 32.512346 0.0369742 1 7 positive regulation of epithelial cell proliferation
112 GO:0060688 0.0364137 32.512346 0.0369742 1 7 regulation of morphogenesis of a branching structure
113 GO:0031102 0.0364137 32.512346 0.0369742 1 7 neuron projection regeneration
114 GO:0010950 0.0364137 32.512346 0.0369742 1 7 positive regulation of endopeptidase activity
115 GO:0031644 0.0364137 32.512346 0.0369742 1 7 regulation of neurological system process
116 GO:0019233 0.0364137 32.512346 0.0369742 1 7 sensory perception of pain
117 GO:0046390 0.0382529 7.039136 0.3116393 2 59 ribose phosphate biosynthetic process
118 GO:0009260 0.0382529 7.039136 0.3116393 2 59 ribonucleotide biosynthetic process
119 GO:0006164 0.0394446 6.916446 0.3169213 2 60 purine nucleotide biosynthetic process
120 GO:0006839 0.0394446 6.916446 0.3169213 2 60 mitochondrial transport
121 GO:0048709 0.0415101 27.862434 0.0422562 1 8 oligodendrocyte differentiation
122 GO:1904659 0.0415101 27.862434 0.0422562 1 8 glucose transmembrane transport
123 GO:0001837 0.0415101 27.862434 0.0422562 1 8 epithelial to mesenchymal transition
124 GO:0010827 0.0415101 27.862434 0.0422562 1 8 regulation of glucose transmembrane transport
125 GO:0090151 0.0415101 27.862434 0.0422562 1 8 establishment of protein localization to mitochondrial membrane
126 GO:0010952 0.0415101 27.862434 0.0422562 1 8 positive regulation of peptidase activity
127 GO:0030516 0.0415101 27.862434 0.0422562 1 8 regulation of axon extension
128 GO:0009117 0.0419590 4.243862 0.7817393 3 148 nucleotide metabolic process
129 GO:0072522 0.0431041 6.572509 0.3327674 2 63 purine-containing compound biosynthetic process
130 GO:0006753 0.0441167 4.155405 0.7975854 3 151 nucleoside phosphate metabolic process
131 GO:0032526 0.0465805 24.375000 0.0475382 1 9 response to retinoic acid
132 GO:0007007 0.0465805 24.375000 0.0475382 1 9 inner mitochondrial membrane organization
133 GO:0015749 0.0465805 24.375000 0.0475382 1 9 monosaccharide transmembrane transport
134 GO:0010977 0.0465805 24.375000 0.0475382 1 9 negative regulation of neuron projection development
135 GO:0035458 0.0465805 24.375000 0.0475382 1 9 cellular response to interferon-beta
136 GO:0008645 0.0465805 24.375000 0.0475382 1 9 hexose transmembrane transport
Module 14
GO_term_cyan <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_cyan.csv")
GO_term_cyan %>%
  kbl() %>%
  kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
  kable_paper() %>%
  scroll_box(width = "800px", height = "200px")
X GOBPID Pvalue OddsRatio ExpCount Count Size Term
1 GO:0030838 0.0000109 102.642857 0.0471609 3 25 positive regulation of actin filament polymerization
2 GO:0030833 0.0000281 72.718894 0.0641388 3 34 regulation of actin filament polymerization
3 GO:0030041 0.0000307 70.433036 0.0660253 3 35 actin filament polymerization
4 GO:0008064 0.0000334 68.285714 0.0679117 3 36 regulation of actin polymerization or depolymerization
5 GO:0030832 0.0000334 68.285714 0.0679117 3 36 regulation of actin filament length
6 GO:0032273 0.0000426 62.559524 0.0735710 3 39 positive regulation of protein polymerization
7 GO:0008154 0.0000461 60.857143 0.0754575 3 40 actin polymerization or depolymerization
8 GO:0110053 0.0000534 57.714286 0.0792303 3 42 regulation of actin filament organization
9 GO:0031334 0.0000615 54.878049 0.0830032 3 44 positive regulation of protein complex assembly
10 GO:1902905 0.0000658 53.561225 0.0848896 3 45 positive regulation of supramolecular fiber organization
11 GO:0051495 0.0000800 49.961905 0.0905490 3 48 positive regulation of cytoskeleton organization
12 GO:0032271 0.0000800 49.961905 0.0905490 3 48 regulation of protein polymerization
13 GO:0032956 0.0000851 48.866460 0.0924354 3 49 regulation of actin cytoskeleton organization
14 GO:0051127 0.0001145 188.714286 0.0169779 2 9 positive regulation of actin nucleation
15 GO:0032535 0.0001205 43.178571 0.1037540 3 55 regulation of cellular component size
16 GO:0043254 0.0001341 41.563492 0.1075269 3 57 regulation of protein complex assembly
17 GO:0051125 0.0001430 165.093750 0.0188644 2 10 regulation of actin nucleation
18 GO:0051258 0.0001564 39.353383 0.1131862 3 60 protein polymerization
19 GO:0032970 0.0001643 38.667488 0.1150726 3 61 regulation of actin filament-based process
20 GO:1902903 0.0001809 37.364286 0.1188455 3 63 regulation of supramolecular fiber organization
21 GO:0007015 0.0001896 36.744731 0.1207319 3 64 actin filament organization
22 GO:0090066 0.0002079 35.564626 0.1245048 3 66 regulation of anatomical structure size
23 GO:0051493 0.0002477 33.415778 0.1320506 3 70 regulation of cytoskeleton organization
24 GO:0044089 0.0003287 30.214286 0.1452556 3 77 positive regulation of cellular component biogenesis
25 GO:0042752 0.0005977 73.236111 0.0377287 2 20 regulation of circadian rhythm
26 GO:0010638 0.0006494 23.694529 0.1829843 3 97 positive regulation of organelle organization
27 GO:0045010 0.0007252 65.887500 0.0415016 2 22 actin nucleation
28 GO:0097435 0.0011797 19.119458 0.2244859 3 119 supramolecular fiber organization
29 GO:0044087 0.0014249 17.858295 0.2395774 3 127 regulation of cellular component biogenesis
30 GO:0030036 0.0014576 17.712000 0.2414639 3 128 actin cytoskeleton organization
31 GO:0030029 0.0014908 17.568027 0.2433503 3 129 actin filament-based process
32 GO:0007623 0.0015416 43.841667 0.0603660 2 32 circadian rhythm
33 GO:0051130 0.0023917 14.790029 0.2867384 3 152 positive regulation of cellular component organization
34 GO:0033043 0.0032381 13.231497 0.3188078 3 169 regulation of organelle organization
35 GO:0048511 0.0037389 27.307292 0.0943218 2 50 rhythmic process
36 GO:0034622 0.0045142 11.697479 0.3584229 3 190 cellular protein-containing complex assembly
37 GO:0007010 0.0057460 10.686975 0.3904924 3 207 cytoskeleton organization
38 GO:0065003 0.0082843 9.303495 0.4451990 3 236 protein-containing complex assembly
39 GO:0043933 0.0120052 8.064205 0.5093379 3 270 protein-containing complex subunit organization
40 GO:0051128 0.0137819 7.641078 0.5357480 3 284 regulation of cellular component organization
41 GO:0045892 0.0232698 10.165354 0.2433503 2 129 negative regulation of transcription, DNA-templated
42 GO:1902679 0.0239515 10.003876 0.2471232 2 131 negative regulation of RNA biosynthetic process
43 GO:1903507 0.0239515 10.003876 0.2471232 2 131 negative regulation of nucleic acid-templated transcription
44 GO:0051253 0.0242955 9.925000 0.2490096 2 132 negative regulation of RNA metabolic process
45 GO:2000113 0.0271218 9.335145 0.2641011 2 140 negative regulation of cellular macromolecule biosynthetic process
46 GO:0045934 0.0278489 9.198214 0.2678740 2 142 negative regulation of nucleobase-containing compound metabolic process
47 GO:0010558 0.0285840 9.065141 0.2716469 2 144 negative regulation of macromolecule biosynthetic process
48 GO:0006508 0.0298147 5.602204 0.7149594 3 379 proteolysis
49 GO:0031327 0.0300782 8.809931 0.2791926 2 148 negative regulation of cellular biosynthetic process
50 GO:0009890 0.0312196 8.627517 0.2848519 2 151 negative regulation of biosynthetic process
51 GO:0022607 0.0345436 5.268844 0.7564610 3 401 cellular component assembly
52 GO:0065008 0.0389387 5.009250 0.7923033 3 420 regulation of biological quality

Figure 2c. Correlating virus interaction and virus-varroa interactions

To test if we can predict the virus-varroa interaction given the virus abundance, we used Mantel-test for correlation between two distance-matrices (Mantel 1967).

# load the two matrices:
# the module–trait association matrix: 
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/moduleTraitCor_66.RData")

# and the viral abundance correlogram:
virusAbundCor_66 <- readRDS(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/virusAbundCor_66.rds")
virusAbundCor_66 <- virusAbundCor_66$corr

# make correlation matrix of the "moduleTraitCor":
corModulTrait_66 <- cor(moduleTraitCor_66)

# (1) Mantel test using "ape" library:
mantel.test(corModulTrait_66, virusAbundCor_66, graph = TRUE,
            main = "Mantel test",
            xlab = "z-statistic", ylab = "Density",
            sub = "The vertical line shows the observed z-statistic")

## $z.stat
## [1] 6.276091
## 
## $p
## [1] 0.001
## 
## $alternative
## [1] "two.sided"
# (2) Mantel test using "vegan" library:
mantel(corModulTrait_66, virusAbundCor_66, method="pearson", permutations=1000)
## 
## Mantel statistic based on Pearson's product-moment correlation 
## 
## Call:
## mantel(xdis = corModulTrait_66, ydis = virusAbundCor_66, method = "pearson",      permutations = 1000) 
## 
## Mantel statistic r: 0.6044 
##       Significance: 0.000999 
## 
## Upper quantiles of permutations (null model):
##   90%   95% 97.5%   99% 
## 0.129 0.170 0.200 0.243 
## Permutation: free
## Number of permutations: 1000
#plot the correlation
#sizeGrWindow(9, 5)
verboseScatterplot(x = corModulTrait_66, y = virusAbundCor_66, main = "Correlation between Fig 2a, \n virus-virus interaction; and Fig 2b, \n varroa-virus interaction", xlab = "Correlation of viral interaction \nwith varroa modules", ylab = "Correlation of viral abundance", abline = T, abline.color = "black", bg = "black", cex.lab = 1.2, cex.main = 1, cex.axis = 1)
Figure 2c. Intra-viral interactions can predict virus - vector interactions.  Correlation model between viral load correlations (fig 2a), and the distance-matrix of the module-virus correlations (fig 2b). For analysis in figure c, Mantel test for correlation between two matrices was conducted using 1,000 permutations.

Figure 2c. Intra-viral interactions can predict virus - vector interactions. Correlation model between viral load correlations (fig 2a), and the distance-matrix of the module-virus correlations (fig 2b). For analysis in figure c, Mantel test for correlation between two matrices was conducted using 1,000 permutations.

In figure 2c, X-axis: how virus interacts with varroa expression, and Y-axis: the correlation of viral abundance across samples.

We found a significant positive correlation between the two distance matrices (Mantel-test for correlation between two distance-matrices (Mantel 1967), Mantel statistic r = 0.604, p = 0.001) (Fig 2c). Meaning, given viruses’ interaction we can predict how these viruses will interact with the vector’s module.